I see the Black Jag uses the A4940 to drive the FETs.
http://www.allegromicro.com/en/Produ.../4940/4940.pdf
I'm still wondering if the tan jag drives the FAN5109's in non-locked-antiphase the way Geek 2.0 described in the original post. It sure looks that way, with the PWMA & PWMB going to the Output Disable in the FAN5109. I haven't checked to see if the firmware source code is in the info I downloaded, and even if it is, not sure I could decipher it.