I am confused by this machine. Seriously. Hoppers, comparators, or repeaters seem to work differently depending on the position. (Not quite sure which thing's fault this is)
I encountered at this specific position, on a bukkit server, with a optifine client. However, I can reproduce in single player on a vanilla client.
I haven't yet tested in the snapshot build, but it is likely this will still exist then.
It may very on position, but I built the two devices on my case at specific places, with the back quartz block that at the given coordinates, the block behind that the lever, and the rest of the machine infront, from f=0 (SOUTH).
Weirdly, if you break and replace the hopper, the problem may disappear or reappear on the other side.
Probably some hash order thing.