Like the ASUS writes, the third PCIe X16 bandwidth is shared with SATA Express storage controller (SATA 5 and 6 ports). You should disable it completely in BIOS to regain 2 lanes for that slot and select x4 mode in 'Advanced\Onboard devices configuration' of BIOS setup.
Didn't even know that setting existed.. I had a good look, too.
It's very easy to assume 'Auto' will do the best for your system, but I guess that's not the case!
Very much appreciated.