Well, I did a complete re-install, slowly added all the mods again and now they work just fine.
Although I did leave out the GWX_DFa-Flag&Pens_2010 mod this time. Might test it with that one later again and will try running Fraps with it too to see if that might have caused the problem.
But for now the keys seem to work again.
EDIT: just tested with the mod. Everything worked fine. Tested Fraps right after that. Still everything fine. So I have no clue what might have caused it, but the re-install has managed to solve it.