yep, for me too it was strange to hear I've got too many versions under the same folder, because I can't imagine not to record a dozen versions (at least) of each project.
On my most used Live set at the moment (on which I had quite often some problems), I have around 22 different versions but the set is quite huge : it's a full repertoire for the stage (the file is around 5 Mo), so maybe it makes too much files to manage for the file indexer.
Anyway, I cleaned some Go from my hard drive, I removed the desktop from Places, I recorded the set in a new location and I erased my Database folder (in the Ableton Library).
Starting from there, I rehearsed today and I didn't encounter any problem.
I'll let you know if it worked on the long term.
Discussion of music production, audio, equipment and any related topics, either with or without Ableton Live