Adding cubes does not sync up with the current game.

In Siftulator, the player can add more cubes by pressing + and -. Unfortunately, I can't get it to work. Either the new cubes are immune to the base OR you have to add at least 4 cubes (and lag up whilst adding them) for the 7th one to actually sync up.

How can I fix this?

ALSO, How can I retain save data of any game upon exiting?