Could it be that the frets are too low rather than the nut too high? Perhaps through wear/playing?
In my opinion Fender has a tendency to leave nuts cut high. Rarely do I find a guitar that has the nut slots cut to the correct depth. Be that Squier or Custom Shop. Obviously the roller nut designs don't have any room to adjust to suit these issues. Which I view as a design flaw of paramount importance. I questioned the designer of the first roller nut that Jeff Beck still uses, Trev Wilkinson, about low fret intonation. His response as I knew it would be was that you must get those slots cut as low as possible to achieve anywhere near accurate intonation on the low frets. Shame he didn't plan for that on the roller nut.
You could cut the slot deeper but it may be pointless if in six months you end up having new frets put on the neck.
Hey Nikininja! Just curious, what is your favorite nut height? I measure from the first fret to the bottom of the string. Stewmac has a nifty tool for this, but I don't own one. I use feeler gauges to stop the files. Stewmac says alot of pros like .010 first string, graduated to .020 sixth string. I think that's quite low.