This has been something I've noticed since the official 1.2 release but may have happened in the beta too.

When I move a full stack of cobblestone (or any item) to a furnace by selecting it and choosing the move all option, if there is a partial stack in my inventory it will fill that stack first and then move what's left over from the selected stack into the furnace. This happens every time partial stacks exist in my inventory and is extremely annoying as I have to then move more from another stack into the furnace to fill the furnace to 64 blocks. The move all should ignore other inventory stacks and move it to its destination.

The same thing happens when moving stacks to chests. It will fill an inventory stack and then move the remainder over to the chest.