Thank you for your post.
It would help if i knew how the file was being accessed. With that said, I was unable to replicate the problem. I took one of my FileMaker Pro 10 database files (file1.fp7), opened it in FileMaker Pro 11 Advanced on Windows XP, turned on Instant Web Publishing, went to another computer and accessed the file through a browser (IWP). I then logged out. I went back to the Windows XP machine and turned off Instant Web Publishing. I am then unable to access the file via a browser (IWP).
Let me know what I'm doing differently from you, and I'll try to replicate the problem here.