Tres Cubano Deluxe CCW : poor intonation

The tres looks great and sounds great, within limits. The problem is that the intonation is out by a mile on the E string(s), assuming GCE tuning. (You can check it by playing the harmonic at fret 12: it should be the same as the fretted note - it isn't). This makes the tres difficult if not impossible to tune: the E at fret IV on the C strings is already about 1/4 tone sharp relative to the open E strings. You might say that this is a feature of all short scale length instruments - and certainly if you listen to professional tres recordings, this marginal 'offness' seems to define the very sound of the instrument - but only to a certain extent. Having said that, all instruments are different, even factory-made ones, and it's possible I've just been unlucky with my instrument.