More the latter, at least for Perl CGIs invoked through IIS. IIS figures out what to invoke for ".cgi" by looking up .cgi in the IIS scriptmap. Typically, scriptmap includes the path to perl.exe, plus placeholders for arguments (the first one of which will be the .cgi script name). Perl then processes the .cgi, sees the -T on the #! line, and complains that the -T is too late.

The trick is to add -T to the .cgi entry in the scriptmap. The full answer is here.

This problem has been around long enough to have inspired poetry.