I recently put light gauge (9-42) strings on my Fender Strat and did a new setup. My truss rod is adjusted perfectly from what I can tell (There's a small gap of about 1mm between the string and the 8th fret when a pushed down at the first and last fret), my action is as low as possible without fret buzz, and I the intonation is perfect when I checked with a tuner while playing harmonics at the 12th fret. The problem is, when I play an F on the E string (1st fret), it's a bit sharp. I checked with a tuner. What is the problem, and how can I fix it?
You might be pressing down too hard.