That is an amazingly beautiful Tardis quilt. Lucky friend !!!
I use mat craft paint, heat set, on fabric all the time and have never had this problem. Did you wash your fabric first? Sometimes the chemicals they put on the fabric won't let the paint penetrate / adhere properly. I think if you repaint now that you have washed it, the paint will stick just fine. But... i don't know about fabric paint...only regular craft paint.