My 2006 madza had same sound ratta .i took a air hose and blewvout both tracks. Then pull on each corner or the glass starting on driver side then passenger. The glass moved about 1/4 inch I then got some on to operate the slider switch and with 2 people forcing the glass to close and the glass started to move about a 1 inch at a time and then still pulsing on the lass we were able to close it completely and it still made the ratta sound as we were closing .also had to push up on the glass and work the tilt to get proper seal. Never end tried to open it again .disconnected wire from the consul switch where the map lots are located.it had nothing to do with index wrong on the motor. Nobody could explain to me the ratting noise it was making.also disconnecting battery also did nothing. To me cleaning the track and forcing it to close because it was jammed in my opinion that why the motor was making that noise because ut could not grab the mechanical mechanism to close .lucky dont know why I didn't blow a fuse. Or damaged the teeth or sprocket