1. build a simple world with hopper timers (2 hoppers connected to each other with an item inside).
2. save it.
3. load it.

Some of timers stop to work. This is because an item which jumps between hoppers start to jump too fast. If you manually remove this item and put it back the timer start to work again until next restart.

Attached a simple world with 4 hopper timers at the X:700, Y:10, Z:-427. I constantly get one of the timer broken after restart.

Also I get constant hang on server stop. Do /stop from the console.

mc.bat contains a script I use to start the server.