My best guess is that the extra bytes could be the windows line feeds (\r\n).
Did you try running dos2unix on the file first? Is the cab file a plain text file?

Anyways, if you want to remove the characters manually, you could just use Tie::File and then chop($tied_file[-1]) twice.
Or slurp the thing into a scalar, chop twice, and then dump it back out to file.