I think I solved the problem but not sure if it's reproducible. It must have been the IBM software/firmware. So I let ServerGuide install on the non-RAID drive, which triggered ibm-utl to update all the firmware. After that, I ran MegaRaid from Windows, and was able to assign drives to RAID arrays, which of course crashed the setup, as the boot drive disappeared. The I reinstalled Win2K12, now with RAID intact.

I am now as far as having installed a new instance of AC 6.0.9. Ready to restore my ENC to it. I put AC on the SSD, running under a 2008R2 virtual machine. Did not see a blazing speed improvement on loading, even compared to AC running on my loaded-down SBS2008. Maybe it will do better on imports.