I can find a bug report about FileMaker bouncing in the dock. I don't know if it's the same issue, but you can check it over for any useful clues:
For More Information see: FMPro won't launch in the background Mac OSX
This is one of many acknowledged bugs that can be found in the Known Bug List thread here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: https://www.dropbox.com/s/jt09b82i0xijbu3/FMP%20Bugs.zip
Actually I was able to fix it by using my ftp program and setting the permissions for enclosed items. I tried this using the finder, but apparently it wasn't applying it to hidden files or folders. Nevertheless thank you PhilModJunk for your prompt response!!