I tried the above workaround but and it works for a bit but after about 1 hour my cpu load jumps back up to 100%. After I shutdown ST3 and then reopen it my CPU usage hits 50% and stays there until it finally jumps to 100%.
The issue with zero length .sst files is an underlying one with leveldb, as far as I can tell. The dev builds (http://www.sublimetext.com/3dev) use a newer version of leveldb that while still not perfect in this scenario, is significantly improved.
btw, this issue is still present with the most recent build (3074). Sublime's been chewing on a zero-byte index file, taking 3-6% cpu all the time... deleting the index file (as per datihein's advice) totally helped to resolve the problem/