Thank you for your post.
FileMaker Pro should not lock up during Instant Web Publishing, and I know that doesn't help you.
It's difficult to determine what is the cause without seeing the script. Is it possible that the script is in an infinite loop? Are you not trapping for the privilege settings? That is, are you using "Get ( PrivilegeSetName) " in your script? Is it possible to modify your script so that you can update a field at certain points in your script? That way, you'll be able to narrow down what script steps may be causing the problem.
Any additional information would be greatly appreciated.