I think this mostly means I am a stupid wheening moron... :-S
In my obfuscated code, I assumed that the same version of CGI.pm would be identical (except for line-endings) on every platform Perl runs on. This is false. But the differences are in fact very tiny (a few lines), and mostly regard configuration parameters, which actually and naturally change between platforms and installs.
I think the Perl core (and CGI is part of the standard distribution) is you best bet at portable code. This doesn't include Obfuscation, that's all... :-)