Since nepomuk was ignoring all my settings I completely moved ~/.kde4 to another location and with the newly generated ~/.kde4 folder nepomuk works as intended. My other problem with KRunner still exists, though (don't want to mix things up: viewtopic.php?f=66&t=108351).

Marked as solved. Good to see you managed to solve it, would still be interesting to find out why Nepomuk was not following it's configuration though.