Same problem here...

Old motherboard...latest bios update 2007, lenovo board.
Has one PCIE-X16 and one PCIE-X1
Card in pcie-x16 directly, works fine.
Card in pcie-x1 works fine
WHEN THEY ARE PUT IN APART ( second slot is blocked by first slot. )
When I put them both in risers... the card, connected to riser onto the pcie-x16 isn't simply found.
VGA is connected onboard.
Also tried with several miners...same problem.

Does a work around exist for it ?   Going to try with a pcie X1  splitter too, and see whap happens.
It's no psu problem...psu is now seeing a load of 20% of rated output.