None of those seemed to have the easiest solution that I know of -- add two dashes at the end of the shebang line:

#!/usr/bin/perl --

This tells the system to ignore anything after that point, so even if you accidentally upload a file from windows to unix in binary mode, it'll run just fine. (although, I don't have a windows machine on the network right now, and I've never tested it with pod, <<EOF blocks, or other multiline strings, which are the only parts of Perl code that might depend on lines being read correctly.)

It should, at the very least, result in better error messages, though, even if it doesn't fix the problem.