It may very well be a combination. My son had them also. And yes they come and go. What happens with growing pains is that the ligaments or muscles are tight. There is no "proof" that it has anything to do with bone growth, but it seems to happen to most kids in the 8-12 yr old range, which coincidentally is when many kids are having obvious growth spurts.
Over exertion or high impact activity (running, jumping jacks, jumping out of swings, or oooh I know.. martial arts where they kick kick kick and run laps and jump knees to hands!).... can cause the muscles to be tight (contract) and put pressure on the ligaments, which can cause "growing pains".. because it still is causing the ligament to stretch more than it "should" to attach the bones and muscles, when those muscles are contracted and don't relax into a normal "relaxed" state.
I have 2 kids in martial arts, and I know what they can do in classes. They don't have to be doing tons of calisthenics to over exert or have high impact. They do all KINDS of drills. Sparring, flying side kicks, crab walks, etc. I doubt it is simple overused muscles (like when we suddenly start exercising and do too many squats and then can't sit on the toilet for 3 days, lol)... it is probably more the "impact" factor. Or so I've read in the past.
I hope she is better soon and doesn't have too bad of a time with it.
For my son, we gave advil and let him soak in warm baths. Many people use massage or heating pads. I would avoid ice paks, though, because that might cause the muscles to contract further...which could make it feel worse.
http://www.itsamomsworld.com/preschool_development_growin...