It took me many hours to figure out which jumper configuration works, but I figured out how to use the VIA 1 to 2 PCI Riser VIA-EXT with the Intel Atom boards:
If you are looking at the riser, PCI gold fingers down, there is a grid of pins 3 rows x 6 columns. The jumper should be vertical between the pins 3rd column right on the lower 2 rows. If you received your riser and haven't moved the jumper yet, just move it left one pin. You can see an image of the riser here at mini-box.com
I hope I added enough keywords that the search bots get this... I searched for weeks to find this info!!!