MSI GTX 970 not being detected on first PCI-E 3.0 slot of MSI Gaming 5 motherboa

Hi guys.
So I recently got myself a new build and some of the components include a MSI GTX 970 Gaming 4G GPU and a MSI Gaming 5 mobo. When installing the GPU to the motherboard I found that for some reason nothing was being displayed on the screen. The screen wouldn't display a no signal message but it would stay black when I booted the PC up. However, when I plugged the GPU into the 2nd PCI-E 3.0 slot it would work and display on the screen. I read on a Tom's Hardware thread of someone with a similar problem and it was recommended to him to check his CPU for bent pins and he later confirmed that was the problem. I have tried the same, but as far as I can tell all of the pins were in their natural state and couldn't find any bent ones.
But I also discovered something else which really started to confuse me... When I plug in my old GPU (a Gigabyte GTX 560 Ti) into the first PCI-E 3.0 slot, it would work normally?! Why would it work fine with my GTX 560 but not my GTX 970?? I have tried everything. Even stripping the pc down to the most basic parts on a wooden surface and tested everything but it's still the same problem. I have also made sure that the display setting in the BIOS is set to PEG, but it would still not display anything when the GTX 970 is in the first slot, but if I plug the HDMI cable directly into my motherboard, even with the GTX 970 installed on the first slot, it would display normally. Also, in my BIOS it doesn't even detect anything being in the first PCI-E 3.0 slot in the Board Explorer menu. But when I installed it in the 2nd PCI-E 3.0 slot the Board Explorer menu would recognize it, but would say it's running at x8 and not x16. Should I be worried about this?
My full setup:
MSI Gaming 5 Motherboard
Intel i7 4790K
MSI GTX 970 Gaming 4G
Kingston HyperX 1333Mhz 8Gb (2x4Gb)
Corsair RM 750 PSU
Corsair H80i CPU cooler
Any advice from you guys on what to do or what the problem could be would be greatly appreciated!

remove power cord from the PSU and do >>Clear CMOS Guide<<
also reseat the card into PCI-E slot 1 and make sure its fill very well into the slot
Quote
MSI Gaming 5 Motherboard
full model is..?

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