Is it rocking front to back or side to side? Are the new wheels aligned so that they are straight with each other? Is the track wore due to the wheels spinning while it sat in one place? Are the flanges on the wheelsrubbing the side of the track (I check mine with a miror on a stick). I go to great lengths to make sure that my wheels are parralell with each other and not rubbing on the track and straight in regard to the track. I use mirrors and straight edges to allign them. Yes it's a pain in the ass. I assume the wheels are new and concentric. The only time I had trouble with the prox missing the home flag was when one side was hanging up and causing the gantry to run crooked down the track and then the prox side ended up doing a wheelstand. When thegantry finally hit the home track stop it bounced and the prox picked up thehome flag.