M. -
I haven't experienced the rocking, but my older daughter (she's now 8) has complained off and on that her legs hurt. I've found that massaging her legs did wonders. It's also a nice chance to spend some close time with her.
There are lots of people in town who can offer some guidance in child massage. My favorite is Amy Sullivan. She's an LMT, and offers pregnancy massage and training for baby and child massage.
You may also want to try some kid's yoga for the stretching and exercise. There are books and tapes available at the library, and again, this can be a great way to have some focused time with her.
It's possible this is about more than sore legs, but start there and see what happens. My daughter is just fine.
I remember having aching legs, too, and my mom would get up in the middle of the night and rub them. I know she was half-awake and probably longing to be asleep, but she was there for me and it's a great memory.