If you package existing sims using SimPE, then when you open Body Shop, make sure you make a clone of the clone, and package that one. Unless something has drastically changed, doing it any other way causes weirdness.
No nothing's changed, shit still happens. When you clone with SimPE, the file sizes are much larger than Bodyshop clones so something else would seem to be getting saved when you use SimSurgery. So recloning with Bodyshop is a Good Idea.