So after a hefty battle i came in my arch-mage quarters.

I turned to my alchemy table and noticed this:
http://imageshack.us/photo/my-images/72/bugsg.jpg/

If you jump in the green you actually fall downwards and you get teleported savely back in the room (thank god).

I tried a different savegame. But this time with no result. Is there a way to "reload" the arch-mage chamber (i moved all my stuff to whiterun).

Bit of a chunk missing there.
Are you using any texture mods or something like that?
Or the the game did not render the texture or the walls properly.
It happens in Oblivion, whilst I running along ahead half the ground is not there. When you got over it, you fall through. To fix it restart the game.

I know I have bug in my game but nothing like that.

i restarted the game and computer, reloaded previous savegames, I turned every mod (better sorting mod) off > no result.

Re-validate game cache through steam?

Welcome to CTD club If you see missing objects, you will soon get CTDs.
http://www.gamesas.com/topic/1318498-ctd-save-file-size/page__st__180