I'm not sure how to solve your problem, but if you deactivate one of those "secondary" graphic card stubs (by right-clicking on it, selecting "properties" and changing the setting at the low end of the box there from "activate" to "deactivate") in the device manager, shouldn't the remaining one turn primary automatically then? Or at least remove any possibility for conflicting commands? Mind which one you choose to deactivate, however.
I take it that the two stubs come from your graphics card standing for the one stub and your onboard graphics standing for the other. If this is true, it might be interesting to know that, when I only had onboard graphics to drive my software, many of the new games I bought didn't start up at all. But when I installed a separate (7600 GT) graphics card in the machine, all games started to work (with a lot more eye candy as well). From this I suspect that your machine somehow has begun to use its onboard graphics to drive games which used to be driven by your graphics card. If that's the case, maybe you need reinstall the whole OS and software package to get things back as they were on your machine. This procedure usually takes care of my tricky problems. This is a time-consuming process, however, and if you do it, be sure to backup all files you want to keep and cannot replace on a separate medium beforehand.