What stepping does your 3960X has? If it's C0, there could be incompatibilities with the motherboard. Even if it worked fine on older BIOSes, there are no C0 retail samples, so they could drop the support for it.
Anyway, do you still have your old UD3? You could force the backup BIOS to make it boot and flash a F12 or F14 BIOS to the main again. I would avoid F15/16/17, anyway.