First, please see Short, Self-Contained, Correct Example - boiling down the code to the minimum needed to reproduce the problem both helps you narrow it down, and it helps us to have less irrelevant code to go through. Also, providing sample input with the expected output would be greatly helpful here.

Second, please see the Basic debugging checklist - I suspect items 3 and 4 may apply here. I would recommend Data::Dump or Data::Dumper with $Data::Dumper::Useqq=1;.

The reason is that I think this could be a line ending issue. I see you're not chomping your lines on input, which I would suggest you change, and if you do that you'll have to add a newline ("\n") when printing the lines back out. Corion already mentioned the possible Windows vs. Linux line endings issue.

There are quite a few other things about the code that could use an overhaul, such as bareword filenames and an unchecked open ("open" Best Practices), seemingly pointless flock calls, predeclaring variables when their scope could and should be limited, but at the moment it doesn't look to me like those are causing the issue.