No real solution here. We have a second MacPro (different model MacPro, otherwise same setup) that has the same issue.
When I want to be able to adjust the virtual faders I knock the real-time playback frame rate down to HALF and then it works correctly. Or, if I am working with 30p material, I just switch the timeline to 29.97fps which also works.
Do you use Fiber to connect to your RAID? Just curious.
2 x3Ghz Quad MacPro
9 GB RAM
Mac OS X 10.5.5
QT 7.5.5
FCP 6.0.5
AJA Kona 3 (6.0.1 drivers)
G-Speed XL 12 RAID