Tracking is important on full scale aircraft because they have multi-cylinder engines that fire more that once per rev.  Our single cylinder engines however always fire with the prop at the same position in its rotation (every one or two cycles).  That means the explosive force is always at the same place and might just be the wrong place for your plane.  Have you tried putting your prop at a different angle?  Full scale will do this at time to see if it has an effect on vibration.  I know we always like to have our prop at a certain place for flip starting but it might be the wrong place for you.  Try rotating it 60 degrees and use an electric starter.