Have you seen these:
Gottlieb System 1: MPU to Driver with diode protection

http://www.bigdaddy-enterprises.com/harnesses/harness-index.htm

If your driver board is the one without the diodes then you should consider one of these to protect your MPU.
At $34USD they are not too badly priced.

I might grab one of those. There was one on ebay last week that I was bidding on but got pipped at the post...don't you hate that?