Searching in the folder reveals "tk2dIndex" is a C sharp file... I'm assuming not to delete that... My guess is that "-tk2d.asset" is the index file...? Anyways my folder doesn't have one; the back up I made before
the 4.1 upgrade does; perhaps that's why it goes into a rebuild loop? I tried installing 1.92 beta and still having issues... I'll try to install from the unity store one more time then I guess I'll have to go back to 4.0.
It appears if I manually rebuild the index it'll delete the "-tk2d.asset" file, throw the exception ... and then complains it can't access it because it's destroyed. (haha). Another one isn't generated so now the project is left without an index file that can no longer be generated. I manually copied the index file from my back up which is fine until I add something and it goes to Rebuild the Index again.
Re-installed Unity 4.0.1f2 and so far everything appears to be running normally. It generates a new index file without exceptions.