Is this with the same riser card? This sort of potential issue is exactly why when I moved my weather software to an ITX system, I went out of my way to get one that still had a PCI slot.
You could try going into the BIOS and try changing the slot detection order, if possible. If another PCI-E slot is available, try that. I just noticed you are using a 64-bit version, have you tried a different Jungo driver version? Do you have a manual for the motherboard and does it say much about BIOS settings? There may be a BIOS setting that will change things, but those are usually poorly documented, at best, and it often takes much research to figure out what they may do.