MSI GTX980 Gaming sometimes not recognized by MSI Z97 Gaming 9 AC

I have been experiencing a very odd problem with my new hardware.
Hardware
Motherboard: MSI Z97 Gaming 9 AC
CPU: Intel Core i7-4790
CPU-cooler: Scythe Mugen 4
RAM: G.Skill RipjawsZ F3-17000CL9Q-16GBZH
Videocard: MSI GeForce GTX 980 4GB GAMING 4G
PSU: Seasonic X-660 80+ Gold
SSD: Crucial M550 2,5" 1TB
Monitor#1: LG 34UM95-P
Monitor #2: Eizo Foris FG2421
OS: Windows 7 Professional
Issue description
The thing is that with 2 monitors connected the videocard is not recognized on a cold boot, but boots perfectly most of the time after a restart. In some cases a restart doesn't do the trick. I have even seen a couple of times that the monitor shows that windows starts and then the monitor loses the signal from the videocard before I can see the desktop (rare). With just 1 monitor attached the videocard is recognized. Als the IGP works fine, it's just the videocard that doesn't seem to be recognized when 2 monitors are connected (all combinations of DP, HDMI and DVI). When the computer has booted after one or more restarts and the videocard is recognized the computer works flawlessly, no problems whatever I do with it (desktop work, stressing hardware, playing games, etc.). Not a single sign of instability.
It's just the cold boot and sometimes the soft boot or restart that causes the videocard to not being recognized with 2 monitors connected.
What makes it really weird to me is that when the computer goes into sleep mode I can wake it up normally within say 10 minutes. But if I wait for let's say an hour the videocard is not transmitting a signal through the videocard.
When IGP is enabled the computer boots and windows loads normally (I hear the sound of the Windows login), although the monitors stay black when connected to the videocard. Then switching the connectors from the videocard to the motherboard shows me a normal Windows login screen, but the videocard is not visible in the device list. When the IGP is disabled to bootup sequence just hangs until a restart works and the computer boots normally with the videocard getting recognized and working properly.
Click sounds
I noticed the motherboard makes 4 click sounds when booting, like relays flipping. I think it has to to with distributing power to al the components, since it looks like components respond to the click by turning led lights on. But I have to say I've never come across a motherboard before that makes click sounds. Is this normal?
Tried fixes
- Replaced the RAM with 100% working RAM from my other computer (Corsair Vengeance LP CML8GX3M2A1600C9) -> problem persists
- Disabed XMP -> problem persists
- Replaced the PSU with another one (Cooler Master V550 Semi-Modular) -> problem persists
- Reinstalled the videocard physically -> problem persists
- Tried several combinations of connecting the 2 monitors to the videocard (all DP ports, HDMI and DVI) -> problem persists
- Replaced the videocard with a MSI GTX970 Gaming (connected with 1xDP and 1xHDMI) -> problem persists
Conclusions so far
The cause can be found in the videocard or motherboard (probably BIOS issue).
Who can shed some light on this issue?

Quote from: JLio01 on 14-November-14, 17:02:39
Try all PCIE slots no luck? Does the black screen always happen on one certain monitor or both?
I tried both the first and the second PCIe slot. No difference except for the fact that in the second slot the card only works at x8 bandwidth.
Quote from: jotan.va on 24-November-14, 18:05:51
BTW - Did anybody try to remove the wifi module from the board and then test?
I didn't install the wifi module in the first place.
UPDATE
I returned the motherboard to the webshop I bought it from and sent my cpu, ram, psu and videocard (GTX980) with it so they could test it. They found out that the videocard is the problem. So now I have to send the videocard to the webshop it bought that from. However, I am suspecting that it's just a VBIOS problem and not some fault in the hardware itself. On the other hand, it would be very strange that MSI would release a videocard that cannot work with one of their own top motherboards, wouldn't it?

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