Both the AMD Radeon setting and GPU Tweak have settings for this, so I would not be surprised if they are interfering with each other.
I've never heard of a motherboard causing the GPU fans to spin up on a discrete GPU. The fans on the GPU are controlled by the GPU, nothing to do with the motherboard. The fans will only spin due to load/temp on the GPU, and any changes you've made in the utilities that control the GPU.
I'd suggest trying the board in another motherboard, but I think that would work and be misleading, as you'd also be running on a system that isn't misconfigured like yours is somewhere. You'd probably have to do a clean install on a spare hard drive to truly prove it's your setup and not the motherboard.
Have you updated the motherboard BIOS yet?