Hi Stratocaster.

A lot of tuning problems on the first three frets are caused by the slots in the nut being badly cut. If the slot is too shallow, the string is too high and has a long travel to the fingerboard. This stretches the string as it's fretted and causes the pitch to rise slightly. As you play further up the fingerboard the angle over the nut is not as great and the pitch difference decreases. If the problem only occurs on one string, this is usually the cause.

Try tuning the open string and then measure the pitch at the first up to the fifth frets and see if the pitch variation drops off. If it does, you need to cut the slot deeper. Be careful not to overdo it or you'll get fret buzz instead.

We once had a very expensive Strat brought into us because the bottom E string was sharp on the first two frets and the shop where it had been bought didn't know why. It took us two minutes to re-cut the nut and the problem was solved.

Hope this helps.

ROG.