I've noticed this happening too. For instance, if using the random Jupiter system, after a collision of moons the new body will have gained a lot of velocity. And if using the new total fragmentation, some of the fragments will launch off into infinity once they start colliding with each other.
EDIT: I may have figured something out. It seems that collisions change the "Rotation Axis" planet parameters, instead of the "Obliquity" parameter. And if the "Rotation Axis" parameter is anywhere other than X0 Y1 Z0, the planet completely spazzes out. This probably messes up the angular momentum calculations the next time it impacts something.