I had a Sky Jump. I never used it with coin mechs, but when my friend bought it, he decided he'd like coin mechs. Installed coin mechs and removed the freeplay jumper on the replay unit.
The 2nd coin chute acts as expected, adding 3 replays per coin.
The 1st coin chute starts a game, but if there's already replays on the replay unit, it decreases once. Obviously, if there's zero replays, it doesn't decrease.
Looking at the schematic for the Subtract "Replay" Unit coil:
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It looks like the coil should fire when the zero switch is closed (eg there's replays), a switch on S and Motor 2C.
Looking at S:
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It activates when the #1 Coin Chute closes via Motor 1C, 2B and the bounce switch, latching itself via 2B until 2B opens.
As far as I can tell, the behaviour I'm seeing is what the schematic says should happen. I guess it makes sense, as a single player game there's no reason to drop a coin if there's replays on the machine.
I don't have another wedgehead to compare to. Is the machine behaving normally?