Cadorman
Ambassador of the Catocaster

Take a look at the bridge. Note the incorrect D string saddle location required to get intonation set. Like I said, brand new strings this morning. Had the same problem with the old string.
Robert, I looked at the frets and they look fine to my eye. This guitar doesn't have high mileage on it. I put the gold hardware on about 2 years ago. The bridge was new and I don't run super low action.