This happens sometimes on Windows, if fairly rarely. Despite a few rounds of trying to diagnose the problem when a system was found to be having it, no universal root cause has been found, that I have seen.

I would try uninstalling Perl, making sure the configuration for .pl and "perl script" file types is fully deleted, and then re-installing Perl. I vaguely recall at least one report of this problem being resolved by some form of re-installing. You might search for prior reports of it for insights more clear than my vague memories on that specific point.

It seems likely that the problem is related in some way to these "file type associations". You can certainly just get these wrong and cause these exact symptoms. But I have seen several cases of this problem happening on systems where no obvious problem with that configuration could be identified (much more often than I've seen systems with the configurations obviously wrong).

You can work around the problem by invoking perl explicitly:

perl myscript.pl arguments go here
[download]

You can also work around the problem using pl2bat (with the various benefits and quirks that go along with that).