Alright,
we found the real issue and it was in our code. We had an unfortunate data set, that caused an endless loop of database calls. The thread abort/interrupt we saw in the Exceptions was basically breaking that loop. It looked like the threads were surviving, but that was not the case, they just kept on spinning on the same message after the AppDomain restarted.
Sorry for bothering you with that and thanks a lot for your help. The restart endpoint was the hint that finally brought us to the right path.
Regards
Michael