Hi Stu,
Please upgrade to FxFactory 2.1.1 which you can download here:
http://www.noiseindustries.com/fxfactory/download/
Also be sure to update Pan and Zoom to version 2, and update the idustrial revolution freebies, both of which are available here:
http://www.noiseindustries.com/fxfactory/free/
After installing all the updates, please launch the FxFactory application (located in your application folder) and check if the two freebie FxPacks are registered. If not, please select them and click register and go through the registration process.
After everything is properly installed and registered you may still have to re-render your timeline in FCP, as the watermark may simply be "burned in" and a re-render will get rid of it.
Hope this helps, please do let us know if you are still experiencing problems.
http://www.noiseindustries.com