It's possible. A brute-force test would be to do a full backup of what you have now, then re-install your system, again forcing it into believing it's a spec Dragon so it gets all the right tweaks. Then redo the same tests to see if they pass now. If they pass, you can do diffs on any of your SQL settings, configuration files, etc. to see what the cause was. If they fail, then you can suspect some hardware problem.

One thing you may want to check before doing all that is the position of the cards in the slots. Verify that the cards are in the same slots we use: http://mythic.tv/annotatedDragonBack.jpg This is just to make sure there isn't any strangeness going on with the hardware. Some PCI cards do seem to have a slot preference, despite the fact that the PCI spec should exclude this behavior.

Other than that, you have access to all the filesystem tweaks we perform for Dragon, so you know everything we do to configure the hardware. I know you've already reviewed them in your previous investigations, but sometimes the eyes skip a line.

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MythiC Dragon v2.0
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I've reconfirmed everything and my cards are in the same places.

Next steps:
I am in the process of building dragon02 with the same specs as my first. (only change from the official dragon spec is the tuner, as mythic.tv was of the hd3000)

I plan to "dragon install" on it and test it in the default standalone manner. If it works, I'll next swap the sound cards to eliminate a soundcard hardware problem. If it works, then I'll go through the standalone config with a fine tooth comb and see where my difference is. It's got to be somewhere!

I'll update when I know more.