Problems with pictures slipping out of sync with audio on a Kona LHe

For the last few months I have been having problems with my edit suit.

For most of 2008 I had been running a very efficient rig, which consisted of: -
Mac Pro 3GHz Dual Core Intel Xeon with 5 GB RAM
Final Cut Studio 2
Kona LHe
Twin Sonnet 500 SATA Towers with 500GB rives
Sonnet Tempo SATA EP4 Raid Controller
Panasonic BT LH1700W monitor
Studiocraft Sprite E8 Audio Mixer
Music Fidelity E101 Power Amp
Cyrus Speakers
We successfully edited several uncompressed SD and HD projects on the above setup.

In January I decided to upgrade the system, as I was nervous about putting mission critical HD data on a Raid 0 Sonnet array. We upgraded to the following:-
Mac Pro Quad Core 2.8GHz with 6GB RAM
Areca ARC 1221X raid controller
10 x 1TB raid tower.
The system was fantastic. Lightening fast and stable until I upgraded the OSX from 10.5.5 to 10.5.6. Now I have a major sync problem.
Monitoring the audio from the Mac audio out – pictures & sound in sync (not good practice)
Monitoring the audio from Kona Analogue Out on the KL Break Out Box - out of sync
Monitoring the audio from Balanced Audio Input vial Studiocraft Mixer – out of sync.

I have trashed FCP preferences, trashed Kona preferences, checked cables and connections and upgraded drivers on all 3rd party devices but nothing has made any difference. Before I take the drastic step to rebuild the Mac, has anyone had similar problems or any bright ideas about how to fix this problem?