Thanks for the information.
I did originally perform a clean install of OS X 10.8.3 followed by a data migration from a system disk to the RAID-0 SSDs on the PCIe card. I currently have the SSDs removed from the Sonnet card and installed in the normal drive bays, and it is running fine and the startup boot-selection screen is again working.
At your suggestion, I will now repeat the clean install and migration while the SSDs are mounted in the standard MP disk trays, and then transplant the drives back to the Sonnet PCIe card and see if that solves the problem.
Would you know if it is possible, while booting/running OS X from the Sonnet RAID-0 based PCIe (external) system, to install bootable Windows using any of the popular methods on a separate SSD mounted to preferably a PCIe card (Velocity x2 - seen as external), or a tray mounted SSD, and have it seen by the boot-manager? Here again, it may make a difference if I do the installation locally from backplane mounted drives and then transplant the drives to the PCIe cards.
Just to clarify ... the RAID-0 array works great either on the Sonnet card or on the Mac Pro backplane (of course it is much faster on the Sonnet card). It is only the startup boot-manager which can't be seen with the Sonnet card, but which works normally when installed to the normal blackplane.
Thanks for your help,
-howard
UPDATE: I passed this information on to Sonnet Support and they suggested several solutions to no avail. I also received a replacement card which exhibited the same behavior. However, I recently received an email from Sonnet Technical Support indicating that they were able to duplicate the problem in their lab, and had opened a Trouble Ticket to engineering which they hoped would result in a firmware update to remedy the problem.
I wonder if this is a issue with just the 2012 Mac Pro models, since others don't seem to have the problem (and I didn't when mine was installed in a 2008 Mac Pro).