Always use strict. Always use strict! With -w you get a warning only.

You are using two variables $cookie, one here

if ( !$sid or $sid ne $session->id ) {
    my $cookie = $query->cookie(
        -name  => 'test',
        -value => $session->id,
        #-expires => ''  makes it so on close session expires.
    );
}
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and the other here:

print $query->header( -cookie => $cookie ), $template->output;
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At the first place, the my variable $cookie is confined to the if () { ... } block, so you are not re-using that at the second place, where $cookie is a package global. See Lexical scoping like a fox.

Thanks for the help, I fixed those errors, pretty dumb of me to miss. The script is now error free, but for some reason it is still not assigning a cookie on my browser, and it seems to think the user is logged in. It is creating sessions on in the tmp folder though. Any ideas on what I am doing wrong?

#!/usr/bin/perl -w
use CGI;
use HTML::Template;
use CGI::Session;
use lib ('/home/scott/intranet/cgi/mods');
use Digest::SHA2;
use DBI;
use DBD::mysql;


my $query = new CGI;
my $sid     = $query->cookie( 'CGISESSID' ) || undef;
my $session = new CGI::Session("driver:File", $sid, {Directory=>'/tmp'
+});  
if (!$sid or $sid ne $session->id ) {
my $cookie = $query->cookie(
                    -name => 'CGISESSID',
                    -value => $session->id );
}

my $template = HTML::Template->new(filename => 'index.tmpl',
    path => '/home/scott/intranet/cgi/intranet/',
    associate => $query);
                                    
my $lg_name = $query->param("lg_nick");
my $lg_psswd = $query->param("lg_pass");
                                
init($session, $lg_name, $lg_psswd, $template);

if($session->param("~logged-in") eq 1)
{
    $template->param(TEST => "YES");
}
else
{
    $template->param(TEST => "no");
}
sub init {
    my ($session, $lg_name, $lg_psswd, $template) = @_; # receive two 
+args

    if ( $session->param("~logged-in") ) {
         return 1;  # if logged in, don't bother going further
    }


    
    # if we came this far, user did submit the login form
        # so let's try to load his/her profile if name/psswds match
    if ( my $profile = login($lg_name, $lg_psswd) ) {
        $session->param("~profile", $profile);
        $session->param("~logged-in", 1);
        $session->clear(["~login-trials"]);
        return 1;
    }

    # if we came this far, the login/psswds do not match
    # the entries in the database
    my $trials = $session->param("~login-trials") || 0;
  return $session->param("~login-trials", ++$trials);
}

sub getpassword {
    # MySQL CONFIG VARIABLES
    my($username) = @_;
    my $host = "localhost";
    my $database = "write";
    my $user = "dbuser";
    my $pw = "dbpass";
    my $dsn = "dbi:mysql:$database:localhost:3306";
    my $dbstore = DBI->connect($dsn, $user, $pw) or die "Unable to con
+nect: $DBI::errstr\n";
    my $prepquery = $dbstore->prepare("SELECT * FROM userlogin WHERE U
+SERNAME='$username'") or die "Unable to connect: $DBI::errstr\n";
    $prepquery->execute();
    my $timestampUpdate = $dbstore->prepare("UPDATE write.userlogin SE
+T userlogin.TIMESTAMP = NOW( ) WHERE userlogin.USERNAME = '$username'
+" ) or die "Unable to connect: $DBI::errstr\n";
    $timestampUpdate->execute();
    my $ref = $prepquery->fetchrow_hashref();
    my $password = $ref->{'PASSWORD'};
        $prepquery->finish();
        $timestampUpdate->finish();
        $dbstore->disconnect();
            return $password;
}

sub login{
    my($nick, $pass) = @_;
    my($password) = getpassword($nick);
    my $encryptobj = new Digest::SHA2 512;
    $encryptobj->add($pass);
    my $digest = $encryptobj->hexdigest();

    if($digest eq $password){
            # replace this check above with something real ie lookup f
+rom a database
            return 0;
        }
        else
        {
            return 1;
        }
}

    $template->param(MYURL => 'http://192.168.1.9/cgi-bin');
print $query->header(-cookie=>$cookie),$template->output;
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I managed to get it to login, the return type on my database was wrong needed to add to the profile such as the $nick and not a false or true value. That seemed to fix it, but it still isnt giving a browser a cookie, maybe it doesnt do that since its a session. Thanks again :)

C:\>perl -Mwarnings -e"$cookie = 6;"
Name "main::cookie" used only once: possible typo at -e line 1.

C:\>perl -Mwarnings -Mstrict -e"$cookie = 6;"
Global symbol "$cookie" requires explicit package name at -e line 1.
Execution of -e aborted due to compilation errors.

C:\>perl -Mwarnings -Mdiagnostics -e"$cookie = 6;"
Name "main::cookie" used only once: possible typo at -e line 1 (#1)
    (W once) Typographical errors often show up as unique variable nam
+es.
    If you had a good reason for having a unique name, then just menti
+on it
    again somehow to suppress the message.  The our declaration is
    provided for this purpose.

    NOTE: This warning detects symbols that have been used only once s
+o $c, @c,
    %c, *c, &c, sub c{}, c(), and c (the filehandle or format) are con
+sidered
    the same; if a program uses $c only once but also uses any of the 
+others it
    will not trigger this warning.


C:\>perl -Mwarnings -Mstrict -Mdiagnostics -e"$cookie = 6;"
Global symbol "$cookie" requires explicit package name at -e line 1.
Execution of -e aborted due to compilation errors (#1)
    (F) You've said "use strict vars", which indicates that all variab
+les
    must either be lexically scoped (using "my"), declared beforehand 
+using
    "our", or explicitly qualified to say which package the global var
+iable
    is in (using "::").

Uncaught exception from user code:
        Global symbol "$cookie" requires explicit package name at -e l
+ine 1.
Execution of -e aborted due to compilation errors.
 at -e line 1

C:\>
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