Try repairing disk permissions (Applications -> Utilities -> Disk Utility). If that doesn't work try logging in as a different user and see if it fails (you may need to build another user account to try this). If it works for the other user account then it is probably corrupted preferences in the original account. Log back in as the original user and delete the preference file located at /Users/<youraccount>/Library/FileMaker/FileMaker Pro 9.0A Prefs
You should also be sure that your OS is up to the latest. You didn't mention what version but 10.4.11 or 10.5.8 were the final versions of those.
If none of the above solve it I suggest de-installing and re-installing FileMaker Pro 9. You can find further instructions in FileMaker's knowledgebase