It seems that the crash is caused by ArchiveInvalidation because at first I forgot to toggle that in FOMM and the game ran fine but without any mods. After I toggled invalidation in FOMM I received the crashing.
The funny thing is that I've been playing Fallout just fine 10 months ago with multiple mods. So why do I have problems now? Could it be that before I used the Unofficial Patch and now I'm using Official Patch 1.6?