This is a bit strange,
Can you provide the model # of the RAID card?
The PCIe slots can come off different PCIe bridge devices on the mother board.
Each bridge and down stream device is configured on power-on to establish the path to from the processor to the end card.
During configuration, the each bridge controller in the system has configuration space that contains pointing information to the PCI bus above it and any PCI bus below it.
(here is were the guess work comes in with out knowing more about the card in use)
I suspect that your RAID card contains a PCI, PCIe, or PCIx bridge and the system is not configuring far enough down the PCI bus.
SInce the x16 slot is on the most direct connnection, it is able to configure more bridges below it than say slot 2 or 3 which have to cross addtional Buses to get back to the processor.