So driving a vessel close (2.2km unpack distance) to another vessel slowed the game down really badly. Turns out I could neither quicksave nor change the vessel nor go to the space center without losing progress (if at all). Opening the log file I read about 8 MB of this
[LOG 20:24:40.838] [KAS] OnSave(Core) Fixed joint detected, saving info...
[LOG 20:24:40.838] [KAS] OnSave(Core) Saving breakforce from saved : 600
[LOG 20:24:40.838] [KAS] OnSave(Core) Fixed joint detected, saving info...
[LOG 20:24:40.838] [KAS] OnSave(Core) Saving breakforce from saved : 600
So even though I undocked the vessel from the mothership the KAS struts I used for stability during transportation - for some reason - had not been unlinked.
Solution was pretty easy: Took an engineer and unlinked the "linked" struts in EVA and detached them (safe is save, you know?). All issues have been solved...
Pro: Easy solution
Con: You need an engineer in EVA. Otherwise fidling around with the savefiles might solve this issue as well...
Anybody ever encountered something similar?