Thanks for adding the code tags.

The reason I asked you to use -vet with cat, was to locate characters that were not immediately obvious but could affect the regex.

Compare

$ cat rogue_char_test
qwerty
asdfgh
zxcvbn
[download]

with

$ cat -vet rogue_char_test
qwerty $
asdfgh^I$
zxcvbn^N$
[download]

On a different note, your MANIFEST.SKIP.bak file has regexes for MSWin-style files (e.g. *.bat and *.com) but your perl -V indicates a Linux(Debian) installation. Did you perhaps copy files from another OS onto your Linux OS? Were the modules you have on your Linux OS installed on that OS (with package manager, cpan or similar utility, or manual build from source)?