For the first time I'm keeping an eye on my chars karma level as I'm using DarN's UI feature to have it listed on the screen. Normally I don't keep track on it whatsoever. Anyway, oddly enough my char went from Karma +2000 (I'm using FWE, which seems to cap it there) to Karma +300 while doing Mothership Zeta. Also, oddly, she DIDN'T get lower karma when she blasted Earth with the Death Ray (just to try it as it's quite awesome - I reloaded from a save just before after doing it). This would explain why Fawkes wouldn't team up with my char during my last play through, which surprised me as my chars are hopeless do-gooders, but she did that part of the MQ after doing Zeta.
This doesn't seem normal to me. I've played with two different Unofficial Patches during these two games, if they are somehow involved in this issue. Anyway, have anyone had or heard of similar issues? Also, is there a way to check this with FO3Edit? It would be nice to know which mod it might be that causes it, as I don't think it's a vanilla issue. It doesn't matter so much in practice as my char in all probability will top out at +2000 after a while again.