updates:
I've installed Reaper and it appears to have the same problem, just takes longer to manifest. After using it for a while, the primary sound card stops functioning. But I can open iTunes and it will have output no problem. To me this is starting to point to an issue with the RME drivers, but that seems unlikely given that they state that up to three cards should work.
Other things I've since tried include:
moving the vid card out of the primary 16x slot and putting the problematic card there. No change in behaviour.
disabling all NIC's. No change.
reinstalling all RME and video drivers. No change
Running the Windows video driver instead of the NVidia driver. No change.
Mobo BIOS is not up to date, but the current BIOS does not address any PCI issues. I may try to update the BIOS, even though I would prefer not to touch it unless as a last resort.
edit to add: when Sonar has the rough start and won't play or react at all, if I crash out of it, go to Device Manager and disable one of the cards, Sonar will then start and play flawlessly.
post edited by tkonecny - 2012/05/31 12:16:13