The third x16 (actually only x8) PCIe slot is indeed usable for a graphics card. Are you connecting the two boards together with an SLI bridge connector? I am unsure that two independent graphics cards will work otherwise...
After I've checked once again all connections (4th time) everything works flawless. It was obviously my fault. Sorry.
By the way: To have two different graphics card in a system (without sli/crossfire) works - until now - without any problem. Even driver installation was easy. The nvidia-package installed both drivers in one go.
Anyway, thanks for your answer and sorry for your effort.