in reply to Comparing two text files
Two things to look at: First, "open (OUT2, ">$matches");" should have an "or die $!" appended to it so that you know for certain whether or not you're even successfully opening the file for output. Second, temporarily change "print OUT2 join(...." to just "print join(..." and visually inspect that the output to your screen is what you think it should be. That in and of itself is usually enlightening enough to help you to isolate the issue.
Dave
In Section
Seekers of Perl Wisdom