I don't know anything about the Shuttle system (isn't that a barebones system?) but from my own experince I would recommend you to get hold of a motherboard without intergrated graphics.
My problems (on two seperate systems with one Geforce 2 and one Savage 3D card) came from a conflict between the built in graphics and the PCI card. I could never get the PCI card to work.
As for a cheap motherboard, all motherboards do have a PCI-slot so just look for one that supports your CPU and RAM.