Hi Jenny,
I'm not very knowledgeable about transplants, but I agree with you that the symptoms you describe are real, and probably don't have anything to do with "muscle weakness because of staying in bed" six months after the fact.
The first thing that came to my mind, if your daughter is still on cyclosporine, there have been numerous accounts of joint pain because of it (you can do a search in the message line of Aplastic Central forum "cyclosporine joint pain").
Also, if she took prednisone, somebody just posted an experience with serious side effects.
http://aplasticcentral.com/test/toas...fid=2&tid=7834
However, because of the establish link between AA and other autoimmune diseases, I would certainly look into that too, maybe asking for a referral to a pediatric rheumatologist. In particular I was puzzled by the "running wobbly" aspect, it might mean many things or nothing.
I would definitely push the doctor to really look into it.
Sandra