Actually shoe rat saved my day! Because shoe rat just commented on the case I am answering it for completeness.
The user enabled the option "Do not keep activities" which lead to this strange behavior, because an activity was killed during the splash screen.
As a future reminder to myself I will get rid of the splash screen because its not holo-style anyway.
Cost me a lot of time to figure this out and i probably wouldn't have found it without your help.