This might partly have something to do with all the day/night changes that happened when the server was small. Mods were given the ability to change the time of day, and when a user or two didn't want it to be night so they could see better, the mods would change it to day. After that, we also had the night time monster hunts. Who knows about now, what with having both the mining world and the main world, not sure of those both count. (Doubt it, since as you said, it sends the time to the clients.) Could also be a bit messed up to you if you were using /ptime when you checked I guess. Just some ideas. I doubt that's really any more accurate, there are so many things that could mess that up. Interesting to know, though.