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Might be a block entities issue? Does this happen with e.g. chests, command blocks, signs, mob spawners?
By invisible, do you mean the hitbox is still there but the textures aren't rendered, or it just disappears allowing you to put another block there? If you can put another block in the furnace's place, does the furnace only reappear when you break the block, or does it reappear automatically?
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Huh, well I guess the server knows it's there, but not the client. Thanks Mojang.
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If you load the invisible furnace so that it should light up, does the client finally display it, or is it still invisible?
There are basically two main reasons for this behavior - either we're sending a bad block metadata and the client doesn't know how to display such a furnace (seen it already before), or the client needs some more data to be sent for the furnace to show up (the block entity) and we're not sending that. The above test should discriminate between the two, since it causes some metadata twiddling.
Is furnace the only affected block, or are there any other block entities that behave this funny ? Chests, enderchests, pistons, ...