No, battery should not affect velocity, except maybe if it is really low, but then it probably wouldn't fire. If you did a compression test with your piston and nozzle, then its probably your hop up. Make sure that ring/oring is there on the barrel.
Also, depending on your chrono, many aren't accurate. Make sure the barrel and hole are parallel and that both the gun and chrono are on a steady base. you shouldn't be touching the chrono or gun unless your firing it, otherwise theres a chance of movement which can completely throw your readings off.
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