I don't see any connection between server usage and the occasional resets. I've used an external MySQL Server (different VHost, same Hostmachine, so latency <1ms) and moved it on the same VHost, but that didn't change a thing (why would it, if the latency difference is about 0.5ms... *scratches head*).
I'm thinking about combining SQLite and MySQL where SQLite is actually used for storing/reading the time, but the time is regularly being pushed to MySQL, too. I only have one server, so that should do it. Although I'm still heavily annoyed by the inconsistency.