Yeah, a pretty dumb mistake. Can apply to more than repeaters, but I only found a problem with them. There's 2 more deep issues I know of in the simulator. One occurs when going back in time after having placed blocks, placing a new block at the same time will delete some of the previous ones. Another one is my ChunkProvider not yet giving back a chunk based on BlockPos. I'm first fixing the latter as it may magically fix the former.
EDIT: Fixed both of them.
EDIT: Fixed both of them.