We just switched to luke-jr's version of pushpool this afternoon, hopefully that clears some up. Bitcoind is always an issue also and when it has problems and needs to be reset you see some stales/rejects.

UPDATE - wont be using luke-jr's pushpoold from git. The stale/reject rates where crazy! Switched back to the one I know works well. My test rig still has 0% stales so that's a lot better. The new LB makes life a lot easier to.