I have a pretty good ear. I fine-tune by matching harmonics on the 5th and 7th frets, as well as the octaves and 12th fret, and the unisons on the 5th fret/next open string. I also have a Korg tuner, which I am also pretty good at using. I first noticed this on a Steinbrenner (sic), then a little bit on a D'Armond Starfire, less on the Guild Starfire, but very much on the Hohner.
I plugged the Hohner into my new Aguilar TH 350 amp and JC cab, and the intonation was right on the nose. Even my "aging ears" could tell the difference. I'm convinced that there is a tone warp demon in the Peavey. Do I call a tech or a priest? ;=)>
Brice HXB-405 Short Scale 5-string; Aguilar Tone Hammer 500; Aguilar DB 285 JC Cabinet; Zoom B3 FX pedal; MXR Blowtorch, Boss RC-2 Looper