| Have you established a witness point? Press down on the string on both sides of the nut to insure the string lies flat in the nut slot. Do this at the saddle, too. Otherwise the string will arc from the rear of the nut effectively changing the scale length.
In some cases, an improperly cut nut will have the same effect. In this example, TDC of the saddle slot is somewhere other than the fingerboard end of the nut. The remedy is to recut the bottom of the slot so that it is flat and sloped toward the headstock.
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Primum non nocere.
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