hmm, that sounds like a biggy of an issue if you are ever jump started aswell, you would have to make absolutly sure they clamped there negative on the case or you could well pop a conventional lead acid,
an altenator is like a conventional generator, it generates an AC voltage, however the larger the load it has to drive, the more force it requires to turn, and the lower the voltage drop from its esr,
so it could be that its demanding so much current that your motor simply cannot turn it, so yes either adding some resistance (moving your alternator negative to chassis may help add 0.05 ohm)
or use some type of mosfet switch to soft start the alternator, where it increases a pwm voltage from it until a certain voltage is met, to stop the current stalling your motor, and the mosfet acts as a tiny series resistance,