Just hit another computer with the same problem. Reinstalled .net 3.5 after using the cleanup tool. Thought it might be a permission problem in the registry so reset them all to default. Ran Sfc through. Scanned with Avast, Malwarebytes,Spybot, Superantispyware, Emsisoft and Dr Web. Found nothing.
Tried right-click and trying to update Adobe Flash player. PatchMyPC reports it downloaded the file. An hour later it was still installing it!
Any ideas for what to try next?