I really can't understand how it would be the spindle, since the spindle runs perfectly if manually connected (not to the G540). I called them anyways... and they had nothing to offer. They said if it works when wired up manually ("simple connections" in the manual), then their side of things works... which sounds reasonable.
I understand what you're saying about 10V vs 5V, but then it should run at 1/2 speed at least.
I'm waiting to hear back from SmoothStepper support too.