I just noticed the above reply to this post.
The issue, for anyone else facing this problem, is due to having the m.2_1 populated with an nvme drive. This disables pcie_2 as well as lowering the link width of pcie_1 to x8. It is not completely documented in the manual, but I found posts and confirmed with technical support that this is the case. From what I have read, running the GPU at x8 does not significantly reduce the performance, so I am glad about that. I will continue to run at x8 with m.2_1 populated.
Thanks for your help and advice.