I am writing this on my A1200 and I got my graphics card working again.
I changed the cards a bit around, and now PCIInfo can see both cards again. I had to this a couple of times in the past also, a bit anoying, but if it works it's alright. Now I have my Voodoo Banshee in PCI slot 2 and my network card in PCI slot 4.
Regarding the jumpers, I think they are set alright, according to the manual. The only jumper that's set is the pins were the boards says 4 MB and 8 MB.
I once tried to install a Voodoo4 4500 in my Mediator. It didn't work. I then got an Amiga 4000 and bought a Mediator for this, and in here the Voodoo4 card worked fine, though the graphics weren't that good as the Voodoo Banshee.