Like Mr. Muskrat, I don't see this problem. You should probably do more debugging and provide more details.

Does your Perl script's file name match *.pl ? What does the command assoc .pl output? If you take the part after the "=" and give it to the ftype command, what does it output? For example:

 > assoc .pl
.pl=Perl
 > ftype Perl
Perl=perl "%1" %*
 >
[download]

Perhaps you somehow got *.pl to be associated with running wperl instead of perl?

I'm tempted to mention "perldoc pl2bat" because that is what I'd use in part because what language a tool is implemented in shouldn't change how you launch it. It might solve your problem just by providing a different enough way to do it, but I doubt it will cast any light on what the source of the problem is.