Seems this is a common problem, that's commonly known by the testufo.com guys, but they have no solution:
Temporarily Turn off Multiple Monitor Mode: Don't Mix Two Refresh Rates
Multiple monitors running at different refresh rates, often interfere with correct TestUFO refresh rate. Make all your monitors all equal to the highest refresh rate, or instead disable multi-monitor.
However, nVidia found a solution and introduced a setting called "Single display performance mode". Guess this simply deactivates 3d acceleration on the second monitor:
Does anyone know if AMD plans to introduced a similar setting? Common use case would be if the hdmi output of the GPU is used for audio output to a receiver / audio device.