Thank you for your post.
Which version of FileMaker Pro Advanced are you using?
If using FileMaker Pro 9, be sure to deactivate before uninstalling. With FileMaker Pro 10, no deactivation is needed. You can just remove the folder.
There are some preference files located in the user account -> Library -> Preferences folder (com.filemaker.* ) but none of those files should affect Adobe Switchboard.