Using Motion Builder 2012 and also tried 2011, the same bug persists without fail.
Using any character rig (Even the one which ships with Motion Builder Mia…)
Add some mo-cap to the rig in Story mode
Play around with a couple of layers and then export or plot the animation so it can be used in normal mode (As a take)
Now if you work with a couple of layers example an additive for the body and an overide to lock a foot placement. It will crash without fail at some point. To be specific, as long as these steps have taken place, MB will crash for sure.
Possible things which I could think would be making this happen are that MB is plotting something during story mode which is building up to the crash later on.
Story mode is just not finished and is not working as it should yet
(But as I mentioned previously, this bug can be repeated in 2011 also)
What could possibly be making this crash, I really don’t think this should be happerning using the official shipped Character (Mia)