It could be excema if you are seeing it on the back of her knees. I believe you will see spots turn up there. I am not sure about them getting darker when she gets hot though, the only place I have delt with excema on my kids is in the diaper!!!
The only other thing I can think of just off of your description would be sceriosis (SP?) My husband has this and his spots reminded me of chicken pox only larger. They would really show up after he got out of the shower and when he was hot. I believe the form he has is gutate, there are several different types.
What I would do is call your ped and talk to one of the nurses see if they think she should be seen. They may be able to tell you over the phone what it is and give you suggestions on what to do.
Hope this helps you a little
A.