Hi Gary,
Except for the raid configuration, I have the same setup as you and the same problem. I can capture uncompressed 10bit 1080i footage all day without issue but cannot capture or playback ProRes 422 through the Kona 2 card without dropping frames.
I did a test and transcoded 1080i footage to ProRes 422 (HQ) and found it would not play back smoothly out the Kona 2 until I changed the Video Playback setting (under Audio/Video Settings in FCP) to “AJA Kona 1080i29.97 8bit (1920×1080)”, a workaround to be sure as picture quality appears to be somewhat compromised. Interestingly enough, playback of the same clip using the “AJA TV” app. looks every bit as good as 10bit uncompressed (to my eyes anyway), and without any discernible dropped frames. Go figure.
AJA support suggested that the problem may be with the speed of the Dual G5 and it’s inability to convert from uncompressed to ProRes and vice versa on the fly. Looks like it’s time for me to upgrade to a new mac (and a Kona3), or the IoHD, or both!
Good luck,
Mike