My apologies for replying to a very old thread, but I haven't found a similar (newer) thread, perhaps only http://forums.iis.net/t/1146580.aspx for IIS 7.
If possible, we'd like to run perl.exe (ActiveState) through the FastCGI ISAPI. We are experiencing major problems with HTTP Content-type headers being sent twice when using the ActiveState Perl ISAPI (perlis.dll, both 5.8 and 5.10) and after a very thorough bug report, in January 2007, ActiveState still hasn't fixed the issue, if it's theirs to fix.
http://bugs.activestate.com/show_bug.cgi?id=67594
In our setup, we run application pools under the IUSR identity, which means perl.exe may not be started by the IUSR. But we have to map the .pl extension to perl.exe for Perl scripts like AWStats. Unfortunately http://www.cosmicscripts.com/servers/fastcgi_perl.html is only helpful if (when) you code your Perl scripts accordingly (using the FCGI module).
Does anyone have an idea?