The most common culprit is a short chainstay length, however, there are different racks that extend further back from the bike than others. I'm currently running this rack: http://www.axiomgear.com/products/ge...racks/journey/ it extends much farther back than my previous rack that I used with a wire basket. However the welds of the Axiom have broken where the rearmost stays come down to join near the axle - solved with heavy duty zip ties to re-attach them, the stays are just to keep paniers from getting caught in the spokes. Check your LBS to see what they have, compare them directly to the one as mounted on your bike and see if that works.
Also, as Prathmann suggests, try to shift your baskets farther back. Good luck.