Hi Rob, I have a C40 configured the same way as yours and it has generated the orange error light upon occasion. I had a disconnect with two pull-out fuses, one to disconnect the rectified dc from the C40, and the other to disconnect the DC from the battery. I found when I plugged in the fuses (i.e. both of them connecting at the same time) the led would blink orange. It could be cured by pressing and holding the reset switch a couple times. I have since re-rigged it so there are two separate disconnects, and I don't get the error anymore when I connect the battery first, then the rectified DC.
I don't think your problem is due to over voltage or over current. I believe the C40 is designed to take up to 125vdc input and 80 amps of current (briefly!).
Curious about your system. What's your wire size in your coils and what do you figure the rpms are? --tom