Ryan,
Just got into your site and checked things out a bit more. I didn't realize that you were running Joomla 1.6.1, but that is almost definitely the cause of the problem. 1.6.5 was the last of the 1.6 series, and there were hundreds of bug-fixes for different issues (and security problems) between 1.6.1 and 1.6.5. 1.7.0 is available now, is the 'newest' Joomla available, and is what we recommend using JFBConnect with.
In particular, even with 1.6.2 (which was the release available when JFBConnect was initially upgraded to support Joomla 1.6+, there were multiple issues regarding URL structure that was corrected with the 1.6.3 release. I can only imagine that those fixes are the same problems that you're running into issues with now with the SEF URL generation.
Sorry I didn't catch this earlier, but our only suggestion for now is to upgrade to 1.6.5 or 1.7.0, both of which should be generally easy upgrades as those are minor releases from 1.6.1 (not like the move from 1.5 to 1.6, if you dealt with that). For more information on upgrading Joomla, see:
docs.joomla.org/Upgrade_1.6.5_to_1.7
Good luck, and let us know if there's any other questions or issues you run into,
Alex