Saber Mage
Comments
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.
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.