I had the same problem on my avid. What worked for me was to do the same process as you described. But I was told that avid can only keep up with about 8000 files in a single Database.
Try throwing away old Precompute files and stuff you dont need. Even after this it took avid a couple tries to get straight. After that i have kept my files down to a minimum and have had no trouble since, well with that at least, its still an AVID. hope this helps.