This bug appears probabilistically. (I don't know the exact cause.)

Put a repeating command block at the border of one chunk, power the command block (with a lever) in the other chunk, save the game and exit. This sometimes saves the unpowered state of the command block.

The same thing happens in the opposite case. After unpowering the command block, save the game and exit. Then, the powered state of the command block is sometimes saved.