I'm at the Ald'ruhn fighters guild and two of the NPC have disappeared. The weapon vendor by the forge is gone and a Nord in a room with a Redguard disappeared after I bought a helmet. I swear when i'm downstairs by the forge I can see a shadow but no one registers. Any clue what is happening? I'm playing a vanilla GOTY on a Win 7 machine.

Use the RA console command to reset the NPCs.

If that doesn't work, you might be having some serious mod conflicts.