|Don't ask to ask, just ask|
I don't think I understand your problem.... or at least, I don't understand why you're "(c)ross-packaging (some) code using PerlApp (9.1.1)." (Why? What's wrong with moving it across your LAN; sneaker-net-ing; or using FTP?
PerlApp does NOT compile your script; it packages it together with it's known dependent modules and what AS calls a "modified" Perl interpreter, but the script still has to be compiled and executed on the target machine.)
My understanding is (in effect) that you're using the "packaging" with the AS utility called PerlApp to move scripts from the Win box to the Mint box... and don't like the way the script looks when you reopen the script in an editor or cat it to a term (or are you unhappy with the font used for whatever OUTPUT the script generates?).
Alternately, I might read your node as a description of moving scripts from the Win box to the *nix box, then running the script on the 'nix box under what you think is "the very same ActivePerl (18.104.22.1684)" and begin dissatisfied with the appearance of the output, wherever you're seeing it.
Are you really sure the Active Perl on the 'nix box was compiled with all the exact same options/libs/etc as the M$ Win version? My reaction is "maybe," but I don't quite buy it... and while I won't spend time researching that, you might want to do so. And, of course, given the way PerlApp actually works, you're likely to have issues with fonts because those on your Win box are NOT identical to the 'nix flavor.
Acknowledged, of course, that both may be mis-understandings.
In either case, please clarify your problem statement. And note also that you've used some very subjective standards ("poor" & "plotting 20 years ago") to describe the problem. Can you provide something more nearly objective -- even, for example, screen shots in dropbox or similar.