Same issues with me. I'm also using Paste, Hazel and HoudaSpot. No issues with Hazel or Paste (yet) but HoudaSpot doesn't find anything. Even searching in one folder SpotLight doesn't seem to work. I've tried the following:
sudo mdutil -ai on
mdutil -Ea
I tried a few other apps that are supposed to rebuild SpotLight which report back that they have finished in about 10 seconds.
Interested to see what the resolution here is.