Had some multi-scale Jackson 7 strings come across my bench. The low 'b' was 15 cents off (sharp) with the saddle all the way back.
I started looking closely at this and discovered the nuts were cut in a way that shifted the intonation point towards the tuners.
Fortunately, the first fret action height was out of spec at .030, so there was plenty of material available to make the necessary changes, and dial 1st fret action in at the .025" spec, but it takes a lot of time to correct this kind of anomaly.