Thank you for your post.
Can you tell me a bit more about your environment. That is, how many files are being hosted? How many clients are accessing the file via FileMaker Pro and Instant Web Publishing? Is everything on one machine, or do you have the web publishing on a separate machine? Do any of the files have custom menus? Do you have any plug-ins installed? Anything else you can provide to help me replicate the problem would be appreciated.