My first reaction is that you have 3 processes running FTP trying to authenticate to the remote server, each with all of their commands buffered up when your script runs ahead and deletes all of the files. A short while later, each FTP process gets authenticated and reads the commands from the input buffer and can't access the files that have already been deleted.

The only thing that makes me think this shouldn't be the case is:

    close (CMD);
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You see, an explicit close on a file handle to a piped command also waits for the subprocess to exit. So the presence of that code should make what I described very unlikely.

My second reaction is "Don't you ever check for failure?!" I can almost excuse a quick hack missing some checks for failure. But once that quick hack starts not working the way you expected, one of the first things you need to do is add any checks for failure that you left out at first. Well, you left them all out:

sub fail {    # Allow failures to show on the web page.
    print @_;
    exit 0;
}
foreach $wmlfile (@fileftp)
    {
      if(-f $wmlfile)
      {
        $ftp_commands =
    "   open $remotehost1
            user $remoteuser $remotepass
            cd $remotepath
        asc
        put $wmlfile
        bye
     ";
         open (CMD, "|$cmd")
           or  fail "Can't fork() to run $cmd ($wmlfile): $!\n";
         print CMD $ftp_commands
           or  fail "Can't write commands to $cmd ($wmlfile): $!\n";
         close (CMD)
           or  fail "$cmd ($wmlfile) failed? ($?): $!\n";
         print "File $wmlfile has been transferred \n";
         print "<br>\n";
         $finish = 'transfer';
         copy ($wmlfile,"./$finish/$wmlfile")
           or  fail "Can't save $wmlfile to $finish: $!\n";
         }
      }
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The error message for close failing is a bit ambiguous because it failing could mean the subprocess returned a non-zero status or it could be some error in the parent process such as not being able to flush some buffered input (thought the subprocess failing seem by far the most likely reason in this case).

Update: I've replaced the calls to die so that the errors would be visible on the web page, since this is a CGI script.

Ah, a Win9x "quirk". I'll have to play with that when I get back to my Win9x box.

So I suggest you add an extra synchronization step. The most reliable I've come up with is something like:

sub fail {    # Allow failures to show on the web page.
   print @_;
   exit 0;
}
$finish = 'transfer';
foreach $wmlfile (@fileftp) {
    if(-e "$finish/$wmlfile") {
        unlink "$finish/$wmlfile"
          or  die "Can't delete $finish/$wmlfile: $!\n";
    }
    if(-f $wmlfile) {
        $ftp_commands =
        "  open $remotehost1
               user $remoteuser $remotepass
               cd $remotepath
           asc
           put $wmlfile
           lcd $finish
           get $wmlfile
           bye\n";
        open (CMD, "|$cmd")
          or  fail "Can't fork() to run $cmd ($wmlfile): $!\n";
        print CMD $ftp_commands
          or  fail "Can't write commands to $cmd ($wmlfile): $!\n";
        close (CMD)
          or  fail "$cmd ($wmlfile) failed? ($?): $!\n";
        for(  0..100  ) {
            last   if  -f "$finish/$wmlfile";
            sleep 5;
        }
        die "$finish/$wmfile not found!\n"
          unless  -f "$finish/$wmlfile";
        print "File $wmlfile has been transferred \n";
        print "<br>\n";
    }
}
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        - tye (but my friends call me "Tye")

C:\Perl\bin>perl file.pl
File x.wml has been transferred
<br>
File y.wml has been transferred
<br>
File z.wml has been transferred
<br>

<--Time delay around 3 seconds-->
<--The file is inside the output buffer to be send-->
<--while waiting to the remotehost to open port or connection,the unli
+nk process has unlink all the files-->
<--when the remotehost has give permission to enter the server,the fil
+es has already been deleted-->
<--So,that's why the error mesage below is sent-->

x.wml: File not found
y.wml: File not found
z.wml: File not found

<--mission 1 which is to send the files to other server is not accompl
+ished-->

C:\perl\bin>
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