There are a few thousand UBB's running IIS5 fast & successfully out of the box so we'll need to look for what's different.
Please check the mapping of .cgi and .pl Either perl.exe %s %s [case matters] or perlis.dll is fine. I doubt, however, the mapping is at issue.
I notice that the scripts run normally when simply reading files -- suggesting there is nothing amiss with the perl or its mapping.
The slow processes are the file write routines. In this case I would check the permissions. These are distinctly different in NT5 [and somewhat confusing if you are just using your NT4 background like me

]
What are the perms in the /ubb directories and their files? RWXD or even full control is required for the IUSR_[computername]. Is there a domain controller involved here? I've seen problems where domain controller configuration overrides the local machine.
Experiment with the permissions making sure the server can at least RWXD in the necessary directories.
Run the ubb_test.cgi script from your zip distribution to see what it says.
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Michael Farris
OpenTopic Product Manager + UBB Enthusiast