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I started a new game (several actually to make sure it was a consistent problem) and the chests aren't spawning items, not even plot items. The dragon cave on emerald island was full of already dead rats and one gold pile (no adventurer's shield or longbow).

Old saves I've loaded up seem to be ok so far, mine carts in red dwarf mines are full of stuff at least, haven't done further testing yet.
Anyone else having this problem?
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This is very strange. Have you tried reinstalling the game?
Just one more question: did you installed any mod? If not, try to install GrayFace patch - it's very useful to fix many bugs.