Most people use a low flaring ball like a spare ball to determine their PAP, and in this case for your tilt as well.  Your tilt typically determines if you have a low or med or high track.  Then from that information they will lay out your regular "strike ball". 

It has been stated by many, that the shape of the core (or perhaps RGs) of your "strike ball", will shift your track, which could be what you are seeing.  Other possibilities include: you change your release for your spare ball compared to your strike ball,  or you could have different pitches in your thumb and fingers (between the two balls) which can promote a higher or lower track.

I think you should throw your spare ball, like you would your strike ball, and look at the track.  That should determine more accurately whether you are a higher or lower track player.

My 2 cents.

Drew