I also have a VIking machine and yes, the center on most all their hoops is not the center of the hoop itself. I got tired of forgetting this fact and started marking the stabilizer once it's hooped if I'm not going to hoop the fabric itself. Otherwise, I place my hoop on my cutting table between marks on the table to align my fabric/stabilizer and hope I get it just right. You should be able to adjust the hoop once it's on the machine to move it to "your" center though.
Most times I'll cut my fabric a bit larger so I can trim it to make the center where it should be once embroidered.