The formatting of the files it not clear.

If you indicate every appearance of a newline by <br> , then the second file does not contain any newlines, and so, the single <F2> will suck in the entire file, giving you the results you seem to have.

It would be a good idea to check if you actualy got somethin in that read:

  defined  my $s2 = <F2> 
       or die "I really need F2 to contain the same number of records 
+as F1:$!";
[download]

To improve readability, please add a space after each "my".