i can't imagine that GIGABYTE is the only manufacturer out there who's motherboards with AMD IGPs don't play nice with discrete nVidia GPUs...though in all my research at the time, i never did find claim of another manufacturer having these problems. the other guy who mentioned that he had the same issues with his GIGABYTE motherboard also said that he was successful in resolving the issue by switching to motherboards manufactured by both ASUS and ASRock. so at the very least, you know you can give ASUS, ASRock, or BioStar a try if you suspect that your current motherboard may be the reason why you can't use both the integrated and discrete GPUs simultaneously (for crunching or otherwise).

Some MB models disable the IGP when a PCIe GPU is installed. I've run into this on a Biostar board. I don't believe that it's brand specific but is model specific or perhaps even BIOS specific. That said, IGPs typically cause the NB to run hot. Running them at max (as in DC) is asking for a shorter MB lifetime. Current IGPs are also so slow that they're crunching performance is pitiful anyway. I'd recommend avoiding DC on an IGP.

Back to the OP: some MBs do not allow using NVidia and ATI together. Some do. If you have a MB that allows them to work together, they will work very nicely. On AMD chipsets just be sure to install the ATI/AMD GPU in the primary PCIe slot and the NVidia card in a secondary slot. It will make the whole process easier.