Saber Mage
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I did not check the server.log; would relevant info still be there, or is it wiped with each server startup?
And yes, I always use both the save-all and stop commands to shut down my server.
I can confirm that I have recently experienced this with my own SMP server. I lost many hours of work because of this bug. I cannot reproduce it, but it took restarting the entire computer the server was on, to fix.
To clarify, new builds do not "disappear" with this bug, but revert to a former state once all users log off, or once chunks are unloaded. The only things that do not revert, of course, are those independent of chunks: Player inventories, ender chests, etc. But all tile entities within a chunk do revert, including their associated data values.
In my instances, nearly every chunk near the world spawn was reverted to its state from over 48 hours earlier.
This causes an issue for me, as I am using the daylight sensor for its unique height as a block, and on top of a hopper. When it is out of contact with sunlight, I expect no signal to be outputted. Because it does output a signal in this situation, however, it causes the hopper to be deactivated more than half the time. I really need this bug fixed. Its functionality is useful in other ways, but please, turn it into a feature which the user must knowingly activate.