Zach Toundas
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I came here to post about this. Mostly horses wearing saddles vanishing, but I have noticed that my small saddle inventory was also missing, thinking I had misplaced it. Seems to happen when my private 1-player server restarts. the auto backup that takes place when the server is turning back on is missing the entity in question, so it seems to be happening during shutdown.
I'll make my specific report, and link it to this one.
I have two versions of this problem. One seems to be very occasional depending on how many entities are in the chunk that is loading, which I get.
The other is when I (or anyone else) is holding a level 4 map. In this case, it is about one stutter per second, including all other entities, too. If I am just standing by some cows, minecarts not around, and have a level 4 map, the cows and any other entities freeze for about .2 seconds every second.
One cause of this problem I discovered was when trying to recover worlds, I had permissions set wrong on the recovered world folder. Use chown to make sure the permissions are set for the user that Minecraft loads under. An easy way to test if this is the problem is to use sudo when running the ./start.sh command. The game should start, but to check its progress you'll have to use sudo again when running 'screen -r minecraft' and it does cause problems with connecting over lan. However, this at least will inform you as to whether or not it's a permissions issue.