I had the same problem (and asked about it a week ago, b/c I somehow missed this post in the Q&A when I searched). What I did was configure IIS to use taint mode Perl (using C:\Perl\bin\perl.exe -T "%s" %s ) with a specific file extension, such as .tcgi or .tpl. Then to make the scripts run taint mode, simply change the extension to whatever you set up in IIS, such as .tcgi or .tpl.