There are exactly two items that determine the voltage at the coil in run, the coil resistance and the ballast resistance. If the voltage to the ballast is in spec that is. Either your coil is internally shorted lessening it's resistance or the ballast is out of spec. Seeing as to how having your ballast plugged in also lowers your start voltage I am thinking is has a path to ground, probably not a clean one though. Out of curiosity, if you remove the ballast from the fire wall (keep it isolated from ground), but leave it plugged in to the wiring harness do your voltages go up?

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They say there is always the exception that proves the rule.
Don't be the exception.