It appears that the problem we have been having with theora and rtp is a known bug. After talking on irc, someone has pointed us to a bug report that seems to be the issue we are having. The good news is that it was marked as fixed. The bad news is that it was fixed just three days ago, so there are no builds we can just grab. We may have to build part of the gstreamer pipeline from source just to test and verify that this is indeed the bug.
Well that is my little update. We have been adding tickets, documentation, and starting to build a plan for the remaining few weeks as well as how we want to start back up during the summer quarter.