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Yup, something's not right there. Almost all guitars end up with the double diagonal pattern that you can see on @>>>>>> guitar above.
How are you testing the intonation? Using the 12th-fret harmonic against the 12th-fretted note?
The only other thing I can think of is that the string is fitting weirdly into the nut. (I'm no expert though)
ffm
Mine's a 22 fret - I'm not sure if that has any difference on bridge placement?