I have a long scale 5 string with weird intonation. From the nut to the 12th fret is 44.5cm. I set my A string to be 44.5cm from the bridge, with all other strings up/ down from this based on string length. I tune up, use a strobe tuner, and can get perfect 12th string harmonics. All the saddles look right. But when I fret the 12th fret, I am sharp. Moving the saddles 1cm backwards solves this. My low B saddle is so far back I can hardly fit it into its slot. Is this right? Should I stay with the theoretically right placement that intones to harmonic, or drop back and intone to fret?