MSI Z170A Gaming M7 SATA Port Issue

[Master Disaster]

I've been having issues with my SATA ports for a while now so today I decided to try and get to the bottom of it and see if I could discover why some ports work while other don't.

 

After messing with SATA Cables for 15 minutes I managed to identify which cable goes to which device and also I managed to find out that any device plugged into Ports 5 or 6 or my MoBo don't work at all. I've tried my BD Burner, an SSD and a Mechanical Drive in both slots but nothing is ever detected? Now I know my UEFI inside out and I can say with 100% certainty that my UEFI is properly configured.

 

My next thought was it might be because I jave an M.2 NVMe SSD installed which is disabling the ports but I've looked through my manual and I can't see anything which suggests that to be the case.

 

Now I'm stumped because I have 5 SATA devices, 2 SSDs, 2 HDDs and a BD Writer which all need to be plugged in however I only have 4 working SATA ports. This is annoying as today I really needed to burn a DVD so I had to swap things around to get the DVD burned working but now I have no access to my Steam HDD so when the burn is done I have to swap them back again. Thing is I know they used to work when I first installed everything.

 

Anybody got any ideas what might be going on here? Is it because of the M.2?