Set breakpoints and step through the code and see what is happening, I suspect it is a matter of timing of events.
Also if I were implementing that I would put the ad rotator inside your usercontrol and embed the usercontrol in layout.master, that way you have a direct reference to the ad rotator and don't have to go fishing for it in layout.master and you can be sure that since it is a child control of your usercontrol its pageload event won't fire until after your usercontrol pageload fires.
Hope that helps,
Joe