You're not using strict, and the script is a horrible mess. I suggest a complete rewrite.

At least the empty file will likely come from $write_data not being what you think it is. It is assigned to by this line of code:

$write_data="$${paramname}:::";
[download]

... and I don't even want to track down to what global variable name is stored in $paramname and where it is then dereferenced to.

Thank you so much for your help! You just proved to me that I need to pass this project on to someone that knows what they are doing. I give up.

#!/usr/bin/perl

######################################################################
+######
# S U B R O U T I N E S
######################################################################
+######
######################################################## 
sub valid_cookie{
    $flag=0;

    my $session_file=$companyrepository."/session.txt"; #file where se
+ssions are stored
    unless(open(INTT, "$session_file")){print "Session not found $sess
+ion_file. $cookie<br>";}
    while (<INTT>){ #find existing cookie
    if($_=~/^$cookie\;/){#if cookie exist
        $flag=1;
            last;
        }
    }
    close INTT;

    return $flag;
}
######################################################################
+###### 
sub writeData {
    my $j=0;

    open (OUT,">".$datafile);

    # Print header
    foreach $head (@header_names){
    print OUT "$head\t";
    }
    print OUT "\n";

    # Print data
    $i=0; # $i represents each row                                    
+                                                                     
+                        
    for ($i=0;$i<=$#write_data;$i++){
    for ($j=0;$j<=$#{$write_data[$i]};$j++){
        print OUT "$write_data[$i][$j]\t";
    }
    print OUT "\n";
    }
    
    close (OUT);
   
}
######################################################################
+######       
sub readData {
    my @temp="";

    open (IN,"<".$datafile);
    $i=0; # $i represents each row
    while (<IN>) {
    if ($i==0){ # ignore the header
        $i++;
        next;
    }elsif ($_=~/^(.*?)\t/){# read in and split tabs
        @temp=split("\t", $_);
        $j=0;
        foreach $t (@temp){ # each column $j in row $i
        $read_data[$i-1][$j]="$t"; # store names
        $j++;
        }
        $i++;
    }

    }
    close (IN);

}
######################################################################
+######       
sub validate_input{
    my $p_name=shift;
    my $p_value=shift;
    my $vflag=shift;
    
    # cosname must contain an aphanumeric character
    if ($p_name=~/col0/){
    if ($p_value!~/[0-9]/){
        $vflag=0;
    }
    # cosnum must be a digit between 1 and 32767
    }elsif($p_name=~/col1/){
    if ($p_value!~/[A-Za-z0-9_]/){
        $vflag=0;
    }
    }
    return $vflag;

}

######################################################################
+######
# E N D   S U B R O U T I N E S
######################################################################
+######

######################################################################
+######
# M A I N
######################################################################
+######

use CGI;
$query = new CGI;

# initial global variables
$repository="/home/warp/userdata/";
$paramcount=0;
$formcomplete=1;
@header_names=("LATA");

@read_data=();
@read_names=();
@read_cos=();
@data=();
@cos=();
@names=();
$error="";

# pluck out some common params that may have been passed
$answer=$query->param("answer");

####check for valid cookie####
$cookie="";
@temp="";
$cookie=$ENV{'HTTP_COOKIE'}; #identify cookie
@temp_cookie=split(';',$cookie);
$cookie=$temp_cookie[0];
($sess_id,$company,$site,$user)=split('%2C', $cookie);
$companyrepository=$repository.$company."/".$site;

valid_cookie();

# If cookie not valid, then redirect to login page
if ($flag==0){print $query->redirect('http://services.genband.com/cgi-
+bin/dbq/na/DBQ_welcome.cgi'); }#redirect to another location 


if ($flag==1){
   $dbqfile=$companyrepository."/dbq_finished.txt";
    if (-e $dbqfile){

    # DBQ has been finished and database has been built
    print $query->redirect('http://services.genband.com/cgi-bin/dbq/na
+/home.cgi'); #redirect to home
    }

}

print "Content-type: text/html\n\n";

# create company specific variables
$datafile=$companyrepository."/latas.txt";

################################
# start html
$header_file = "header1.html";
open(FILE,"$header_file");
while(<FILE>) { print $_; }
close FILE;

print <<'ENDHTML';

<tr>
    <td width="1020" bgcolor="#f4f4f4" align="center">
    <table width="900" border="0" cellspacing="0" cellpadding="0">
    <tr>
    <td bgcolor="#232021" height="25px" width="499" align="left" valig
+n="bottom"><p class="h1"><a href="DBQ.cgi?tab=1#TabbedPanels1">Call P
+rocessing Resources</a> : LATAs</p></td>
    <td bgcolor="#232021" height="25px" width="401" align="right" vali
+gn="bottom"><p class="blinks"><a href="logout.cgi">Logout</a>&nbsp; |
+ &nbsp;<a href="DBQ_setPW.cgi">Add User</a>&nbsp; | &nbsp;<a href="co
+ntact.cgi">Contact</a>&nbsp; | &nbsp;<a href="comment.cgi">Comment</a
+></p></td>
    </tr>
    <tr><td colspan=2 align=left bgcolor=#ffffff class=border2 class=b
+order2> 
    
ENDHTML
    
# if the screens file exists then we have already been here once and s
+aved valid data, read this data in 
if (!$answer) {
    if (-e $datafile){
    readData;
    $formprocessed=1;
    }else{$formcomplete=0;}
}

# process passed parameters
foreach $paramname ($query->param) {
#    $paramcount++;
    $paramvalue=$query->param($paramname);
    $$paramname=$paramvalue;
    $$paramname =~ s/\s+/_/g;

    # place the values in the appropriate array location
    if ($paramname =~ /row(\d+)col(\d+)/) { # row(i) and column(j) as 
+read from webpage
    $match1="$1";
    $match2="$2";  
    $write_data[$1][$2]="$$paramname";
       
    if ($match2==0){
        if ($$paramname=~/[0-9]/){ # validate name
        push @fail, $match1; 
        }
    }
    if ($$paramname=~/\D/){
        $formcomplete=0;
        $error="Lata value must be numeric";
    }
    }
#    print "$paramname, $$paramname, $paramvalue, $$paramvalue<br>";
    if (($paramname eq "answer") && ($answer eq "finish")) {
    $finished=1;
    }
}

# trunkate list where Profile names are undefined
$len=@fail;
@write_data = splice (@write_data, $fail[0], $len); 

#####################################################################
# if the finish button has been clicked                             #
#####################################################################


#####################################################################
# when entering this page from the main DBQ the answer will be null #
#####################################################################
if (($finished) && ($formcomplete)) {
    writeData;
    print "<form action=DBQ.cgi?tab=1#TabbedPanels1 method=post>";
    print "<p class=status>";
    print "The class of service data has been saved. Please click next
+ to continue. <input type=submit name=answer value=next>";
    print "</p>";
# if we are arriving from the main page, a next or re-submit button wa
+s clicked, or there  
# was an error in the form when the finish button was clicked then red
+raw the  

}else{
    # if we are here from the main page and this form has been process
+ed before then print this message  
    if ($formprocessed) {
        print "<p class=main>";
        print "The Class of Service form has already been processed at
+ least once, the data last submitted is below.<br><br>";
        print "</p>";
    }
    
    # print instructions
    print "<p class=status>";
    print "In the table below is a list of the termination types that 
+will be data filled in the switch. ";
    print "To define a Class of Service, provide a name in the box at 
+the top of the column and then to the ";
    print "right of each termination type click the check box to allow
+ that termination type ";
    print "for the given screening class. An uncheck box will indicate
+ that the termination type is to be ";
    print "blocked for the screening class. For more details click the
+ help button.";
    print "</p>";

    print "<hr>";
    print "<form action='latacfg.cgi' method='post'>";

    # present form
    print "<div style=background-color:#ffffff;overflow:scroll;width:9
+00px;text-align:top;border:1;>";
    print "<table cellpadding=0 cellspacing=0 border=0 style=margin:.1
+in;><tr>";
    print "<th class=\"mess left_border\" >LATA<span>Specify the LATA 
+in which you will be providing service.</span></th>";
    print "</tr>";


    # Print rows    
    for ($i=0;$i<=10;$i++) {
    print "<tr >";
    for ($j=0;$j<=0;$j++){
        $type="";
        print "<td align=center>";
        $paramname="row".$i."col".$j; 
        if ($read_data[$i][$j]){
        $type="<input style=text-align:center type=text size=17 maxlen
+gth=16 name=$paramname value=$read_data[$i][$j]>";
        }else{$type="<input style=text-align:center type=text size=17 
+maxlength=16 name=$paramname value=$$paramname>";}
        print "$type";
        print "</td>";
    }
    print "</tr>";
    }

    print "</table></div>";
    print "<div style=margin:.2in>";

    # initial presentation of the page
    if ((!$formcomplete) && ($error eq "")) {
    print "<input type=submit name=answer value=submit>";
        print "<button type=button type=button type=button onclick=\"w
+indow.location='DBQ.cgi?tab=1#TabbedPanels1'\">";
        print "cancel</button> Click 'cancel' to return to Main Menu w
+ithout saving your data.<br>";
        print "Click 'submit' to proceed with this form.";
    # errors found when processing
    }elsif((!$formcomplete) && ($error ne "")){
    print "<input type=submit name=answer value='re-submit'>";
        print "<button type=button type=button type=button onclick=\"w
+indow.location='DBQ.cgi?user=$user&amp;company=$company'\">";
        print "cancel</button> $error";
        print "Click 'cancel' to return to the Main Menu<br>without sa
+ving your data or";
        print " please make corrections and click re-submit to proceed
+ with this form.";
    # form has been completed without errors
    }elsif ($formcomplete) {
        print "<input type=submit name=answer value=re-submit>";
        print "<button type=button type=button type=button onclick=\"w
+indow.location='DBQ.cgi?tab=1#TabbedPanels1'\">cancel</button>";
        print "<input type=submit name=answer value=finish> ";
        print "The data on the form has been validated. Click 'cancel'
+ to return to the Main Menu<br>without saving your data,";
print " click 're-submit' to make changes, or click 'finish' to save y
+our data and return to the Main Menu.";
    }



print "</form>";

}
print "</td></tr>";

print <<'ENDHTML';
</table>
    </td>
    </tr>
    <tr>
    <td colspan="4" height="25px" bgcolor="#f4f4f4"></td>
    </tr>

    <tr>
    <td colspan="4" height="25px" bgcolor="#F0251A"><p class="h2">&nbs
+p;</p></td>
    </tr>

ENDHTML

    $footer_file = "footer1.html";
open(FILE,"$footer_file");
while(<FILE>) { print $_; }
close FILE;
[download]

I don't even see where in the script you would have an "upload" functionality. Maybe you should cut down the script to 10 or 20 lines and start working from there. Also this HTML:

...
<form action='/home/warp/userdata/$companyrepository' method='post' en
+ctype='multipart/form-data'>
...
[download]

is quite unlikely to work, unless your webserver actually serves a directory /home/warp/userdata/..., which very few do by default.