Hi Tord,
had you tried connection with Sabre reference boards ?
In general this may be related to signal loss due to board material
and layout. One can try to tweak signal strength with IOMUXC GPR8
as described in AN4784 AN4784: PCIe Certification Guide for i.MX 6Dual/6Quad and
i.MX 6Solo/6DualLite - Application Note
Best regards
igor