I may have been looking at this backwards some. Are you saying that the index page created by IIP has a higher user count than your main index page generated by ubbthreads.php?
Are you using the aprove new users feature? I think I see a problem then with the index page. I'm counting everyone, including unapproved users.
I have updated the zip attached to IIP's main post. Just download and upload the new index page. Let me know if that fixes the problem. Thanks.