I confirm that this is a bug in the vanilla server- I suspected an issue with the bukkit port at first, but a completely clean vanilla server suffers from this as well..
However, I can't see why this happens. It looks like everything is practically identical between say IronFurnace and the regular furnace.
SMP?
OK, I've found the problem: the server side Containers need to override onCraftGuiOpened and update the state of the client by using icrafting.updateCraftingInventoryInfo for the three progress counters. If you refer to the vanilla furnace you can see that it has this behaviour.
I suspect that under the covers ModLoader.OpenGUI was doing something similar prior to your changing to not use that on the server side.
Note updateCraftingResults is not going to update in precisely the case we see it bugging out- namely when there is no work going on, because the container's progress fields will match the tileentity's in that case, and so won't send the updateCraftingInventoryInfo, and that's probably why the furnace works and your containers don't.
How to fix this? 
I'll talk to Player, he did the GUI code
