It's really common for people with flat feet to overpronate (sometimes severely so). When she walks, do her ankles look like a C? If so, she might benefit from orthotics. The problem is, if your feet are out of alignment, then the foundation for your whole body is out of whack and it just travels right up through your body. Most running stores have orthotics. They usually have like a machine that you step on or a treadmill that you walk/run on and then the computer tells you what ones you need. You can also get custom ones and heat moldable ones done, too.
OP - I'm sorry it looks like your daughter's arthritis is rearing its ugly head.
I hope she feels better soon, and her rheumatologist can find the right combination of meds and PT for her. <3