Small (potential) clarification.

The winNT box probably had a file association (the NT ~equivalent of shebang lines) set up as:

assoc .pl=perl_script
ftype perl_script=c:\perl\bin\perl.exe -w %1 %*
[download]

Which means that your scripts probably were being invoked with -w.

If you choose to use DirtyDamnApe's one-liner to update your CGI script shebang lines, it would make sense (from a security point of view) to make them -Tw to enable taint checking. (See perlman:perlsec)