Thank you for your post.
I have not noticed any slowdown with FileMaker Pro 9 with all the Security updates installed, and I know that doesn't help you.
Are you using any additional plug-ins? If so, try disabling them and see if this helps. If so, check with the manufacturer for any updates.
Since FileMaker works closely with several system files, I would then suggest uninstalling FileMaker Pro 9, remove the FileMaker Pro 9 folder (if not done automatically) and reinstall FileMaker Pro 9.