I'm sorry... after reading "two Xeon 5690 CPUs, 144GB of RAM and 8 Zotac GTX 580 cards with 3GB of RAM each" my brain shut down and I couldn't stop drooling.
Such a system is a million percent out of my league.
No idea what the issue is. My best guess is that you broke a performance barrier- the system was operating so fast that it actually appeared as if it were slowing down.
Yup, I'm certain that is what's happening.