I believe I've lost large amounts of rep (~100) without it actually resetting to 0 before. I lose my rep almost daily it seems, on multiple toons. I've had it happen without logging out.
I'd be looking for bogus time values in your decay algorithm. Perhaps a negative signed integer being converted into a large unsigned integer or such. I seem to recall there being a bug with huge negative reps in beta as well, chances are the bugs are related if you guys only implemented a hack to prevent the negative reps without actually figuring out what was causing them.
I hope you have a way to give us back all our lost rep too.
