Have you installed Windows in UEFI mode with GPT bootsector? If not erase the disk and reinstall drivers.

Have you tried different version of risers?  My latest batch of 006c risers have really crappy USB 3.0 cables and only work in some PCIE slots.
I've just build 4 MSI B250 PC mate rigs and all 4 only worked with 3 video cards. Two center PCIE slots needed older risers.