This makes no sense to me,
everything ought to be physically the same, alignment, positioning of heads and tracks, reel tables height, electronics also identical, hmmmm
Any clues from the VU meters when playing?
Any error, wear, alignment, bias, ought to be the same for either pair of tracks, it's the same heads in same position reading them.
Maybe talk to, or write to Jim, asking him what he thinks it could be.

