Just a guess, but I'd suspect it could be the OS.
Would you be willing to try using Mavericks (10.9.5) on the 5,1?
CS6 is getting old, 5,1 is getting old and neither were optimized for 10.11
I will try that next.
Quicktime 7 playback performance is identical between the two machines. They both cannot get better than 12-14 fps on Cineform 4K Raw files.
Yet, the older, slower i7 handles the Cineform perfectly without any dropped frames in Premiere CS6 at 1/2 res. The Mac Pro 12 core just can't do it, even at 1/16 res which is mind-boggling. Geekbench scores are 1806/6909 for the i7 and 2506/27300 for the 12 core. So CPU even at single core shouldn't be an issue.
A trial of CC on the Mac Pro did no better.
The problem has something to do with Cineform Raw and Adobe QT32 server.
When booting from the drive that contains the working system, everything works smoothly.