The one thing I notice about your code is that you have three loops that read from <>. It is possible that some difference in the input results in the inner functions reading extra data. t is also possible that you missed a spot when changing the code so it was reading from a different file handle. You might want to add debugging code to print the line number and file for each line to see that the right file and lines are being read.

print STDERR "$ARGV:$.:$line";
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I would suggest rewriting the code so that there is only one loop that reads lines. Use flags or a state variable to control the processing. This makes it easier to analyze where the file is being read and what the state the processing is in at each stage.