I fear that without any sample code to reproduce this problem, we will not able to help you - the soothsayers have spread their wisdom for the month, the ESP-reader was frozen by the snow and the bird watchers have no birds to watch.
Copy your script to a different place, and verify that the error still occurs. Then start deleting lines, until the error stops occurring. Then slowly start adding lines back in, and try to keep the error away. Maybe brian's Guide to Solving Any Perl Problem can be of help. I would recommend you move away from IIS, to exclude the possibility of ActivePerl / PerlScript / ISAPI being the problem first. If that removes the problem, the problem likely is not with Perl, but with PerlScript / IIS / ISAPI.