I had the same issue and it was resolved by a total bike fit. We adjusted my saddle height, shifted it back, moved my cleats up, moved my cleats out and switched me to Aline Insoles. Can't tell you which one helped with the pain you are describing, maybe it took them all!
Amanda
2011 Specialized Epic Comp 29er | Specialized Phenom | "Marie Laveau"
2007 Cannondale Synapse Carbon Road | Selle Italia Lady Gel Flow | "Miranda"
You don't have to be great to get started, but you do have to get started to be great. -Lee J. Colan