Now this is a total shot in the dark, but I think the Lucy the Wyvern mod MIGHT have something to do with it. I really don't know, though - this is just a guess, and not even an educated one.
What I'd do is try if this happens to other familiars as well - use the ones for neutral alignments, though. If it doesn't, go get Near Infinity if you don't have it already and look up FAMPSD.CRE and FAMPSD25.CRE and change their race to NO_RACE. (EDIT: Maybe change the class as well.) The Fairy Dragon could use the same treatment. Of course, since testing this might take time since you said it wasn't the first time the familiar was out of the backpack, you might want to do that anyway. (For testing purposes, you could change your current characters alignment and CLUA in the appropriate familiar. But this might not prove to be very enlightening.)
Oh, and while you're at it, you could check if there are any scripts assigned to the familiars. They're not supposed to have any at all.
Edited by The Baboon, 25 October 2009 - 04:35 PM.