This was a real pain in the ass because I didn't realize I only had two RCS thrusters instead of four on the transfer stage. So docking was limited to two-way movement. Good thing MechJeb lets you align to target, because I kept doing that until it clicked. Worked out in the end, got the ladder from the observation/docking pod lined up perfectly with the command pod.
Lesson learned, check your RCS! I'll make sure that payload rocket is fixed next time I send it up. :P