Hi everyone, I have recently got a X299 Dark and have encountered an interesting problem.

My cooler is Noctua D15, so in it's usual configuration it covers the top most PCI-E port, hence the GPU has to go to any of the other ports. 
But, the three bottom ports have a SATA connectors to the right side of the mobo and my GPU (MSI GTX 1070 Gaming X, it's 279mm, just a bit above average i guess) hits those connectors and cannot properly sit in the those PCI-Es. It won't lock or boot (D6 and A2 errors). 
The bottom most port is free of those SATA, but in my case it is way too close to PSU to fit a card. 
 
As seen in the photo, brute force did not work. 
And yet all the it needs is really just a fraction of a millimeter to fit. That's just frustrating and seems to be quite a design flaw in mobo layout. My previous X99-E ASUS had no issues fitting this card in any PCI-E, since SATA connectors were just positioned higher.

Else, if someone had the same issues, what are possible solutions? (vertical mount won't work in my case) and a riser seem to be an overkill

My current solution is to have D15 rotated vertically (it's a bit slimmer this way), I have also removed the GPU backplate and now it can fit in the top most slot and works fine. But, the airflow of the system is now screwed. It's not too bad numbers wise, but it looks and feels messy.
Also funny that the SATA connector blocking the second PCI-E is legacy SATA, so I don't think anyone is actually even using it...

tbh I don't think there's any solution not involving buying stuff or voiding the mobo warranty, so it is more of an information post for people looking into buying this mobo. Since D15 is a popular option for top tier air, and longer GPUs aren't exactly rare, that's something to be aware of. 

Cheers
 
p.s. another tidbit of fun is the topmost GPU lock. If you have a big aircooler (in normal horizontal config), it is pretty much impossible to get to, so to get GPU out, you have to dismount the the whole cooler. You can kinda hit with the screwdriver, but chances are, you are just going to break the lock (like I did). 
Better fun yet, as middle fan in D15 covers the cooler screws and if GPU is mounted right beside it, you need to get a fan out of the cooler...but you can't actually do that. And you can't release a GPU, because of the lock. 
It is my first day with this review approved, all around praised mobo, but damn I manage to find a lot of flaws in it :D

Thanks, 
Maybe I wasn't clear in some regards, the problems aren't in the cabels, there's nothing plugged in to the first Legacy sata (the ones plugged in the picture are SATA 0/1/3), the issue is SATA connector (black box) height, its just a tiny fraction higher than it really should be and thus does not allow me to install the GPU. 

By spec, PE4 is also x16, but is again has SATA clearance issue, so you don't have to use the top port all the time and as I said, it is normal for high end air to cover top PCIe, sort of the price for performance. 

As for the case its midtower Phanteks Evolv. It isn't really small, the port I talk about is PE6, which is not meant for GPUs anyway. It will fit any other extension just fine. 

Not a Case I would use myself with the X299 Dark.

Again, cables are not the issue, they are behind the gpu and it does reach them.
Case wasn't bought for this mobo, it's a rebuilt system from x99, to which it was just fine.

Generally however, something bigger with better airflow would sure be preferable.

GGTV-Jon
As for his GPU / Sata issue he was saying the card hits the Sata connector housing before latching into the PCIe slot. Sounds like it is not a good tolerance fit between the Dark and that particular GPU.

He would have to see if he could make some modifications to the GPU, or buy an EVGA card that actually fits

Or is pushing down the Motherboard PCB and not holding the Back Side of the Motherboard and applying pressure while installing the GPU.

Dark designed to follow PCIe mechanical specification, including SATA connector clearance. Meaning that PCIe card that comply with spec should fit correctly in the slot, without touching anything. I'd say it particular combo issue, and looks like backplate is a tad off. Maybe alternative is to loose backplate mount and try to tighten it that one millimeter higher on VGA PCB, so it clears the port?