Z97P-D3 Issues with PCIe x16 Slot

[Hirog]

Hi,

I built me a new rig with the Z97P-D3, a GTX 970, i7-4970K, WIN10.
When the graphics card is put in the x16 Slot randomly on startups I only get 2 beeps with a short delay in between, a longer delay, 3 beeps in fast succession. If I didn't misinterpret it it signals a problem with the graphics card.
If the System starts the Gaming Performance is very weak, 5-20 FPS on lowest settings, a 4.3 rating in Windows experience rating. Also the "Kernel time" spikes massively in the  task manager, from around 1-3% to 30-40%. GPU-Z showed 40-60% utilization on the GTX970.
I tried to exchange the Power supply in case its faulty (Thermaltake Berlin 630W), no change.
I plugged the graphics card into a x16 Slot on a different PC, worked like a charm there.
I updated the BIOS, tried different Driver versions, no change.
I put an old graphics card (Radeon HD6670) I had into the x16 Slot, worked perfectly fine (40-110 FPS, 7.5 experience rating).
Setting the PCI Settings from Auto to 3.0 in the BIOS didn't help either.

I put the GTX 970 into the PCIe x4 Slot, it works perfectly fine there (60-140 FPS with 40-50% utilization), so only the x16 Slot is making problems for it.

Did any1 experience something similar or has an idea what it could be coused by?
Hoping its not a Hardware defect...

[autotech]

iwould email gigabyte support as sometimes they have a bios for certain graphics cards. otherwise you are looking at a bad slot or a wrong bios setting.

[Hirog]

I could narrow it down to beeing a problem with PCIe Gen3, on Gen2 the card works perfectly fine in the x16 Slot.
My other graphiccards only support 2.0, so does my other mainboard, so I can't test if its an issue with the card or the board...