What version of FileMaker do you use?
And what Operating System version?
Windows XP Pro.
Ok, then I may have the answer. We use FMP 10 extensively here on XP systems, and what slowly creeps into them is a gradual loss of the ability to manage multiple open windows. Dialogs, browser tabs and applications windows refuse to open and sometimes fail to display properly if FileMaker is running. At first, you can close a few extra windows and then things will work again, but it get's progressively worse until you can't open any extra windows with FileMaker and sometimes FileMaker will crash when you initiate a script that should open a window or dialog.
For us, the solution has been to uninstall and re-install FileMaker. That cleans up the issue for quite a while, but it then gradually recurs.