This sounds like an INI file type of problem. Not the system or user INI files, but a private INI file (whose exact name I can't recall but may be 'C:\mozilla.org\mozilla\registry.dat') for Mozilla. Could be lots of things from a disk glitch to a very low freespace situation.
After you repair things (or now if Mozilla is working fine) make a copy of that file somewhere else. Then, the next time the problem occurs, take a look at the current 'real' registry.dat and see if it's corrupted. That may provide more insight into how to correct the problem.