Same here, after updating to 10.11, "populating games" phase takes forever (over 5 minutes). same with 10.12 beta.
I tried reinstalling 10.10, and works like a charm.
The problem is that, during startup, I noticed that 10.11 takes 100% resources from H: drive (the one where i put the roms), like if it was checking the rom files, where 10.10 doesn't