So I recently installed Bem Cavalgar through old Knossos and since then I've encountered (at least) two bugs. The first is that none of my installed mods could recognize my joystick. I eventually managed to fix this through the in-game options so it's not a big deal. The second bug is more serious.
When opening a mission I was working on through the MVPS I was immediately hit by a wave of error messages relating to invalid docking ports and the GTF Ulysses. When FRED finally came to, I saw that many Terran ships, including several transports, had been turned into Ulysses fighters with completely default weapons, etc. I exited out of FRED and opened up the mission in Notepad. There I saw that nothing had actually been changed in the mission data; every ship was the model it was supposed to be.
These FRED errors have not appeared consistently. I have reopened the mission in FRED twice without incident. It could be that something just got temporarily confused. Something that might be relevant is that I did play Freespace 2 some while Bem Cavalgar was in the process of installing. Maybe that screwed something up.