I'm not sure what the cause might be, but upgrading from 1.3 to 1.4.1 causes certain parts of my model to freak out. It looks like its trying to be pulled in many different directions at once, causing it to distort and spin wildly. When settled, those parts are twitching constantly.
It seems to specifically be parts several links down a chain of links and that all have the same origin point: For example, I have a ribbon that freaks out that's tied to the base of the tail on my model with three parts that all have the same origin point. A similar ribbon tied to the end of her braid does the same thing.
I'm finding it might have been related to a few issues pertaining to bounce force and gravity being different from when it was originally rigged, as well as the fact the model was just plain LARGE (massive resolution that had to be zoomed out to fit right) which was causing some performance issues when all combined.