First, check your tuning. Affix a capo at the first fret and depress the fourth string at the last fret. With a feeler gauge, check the gap between the bottom of the string and the top of the 8th fret—see the spec chart below for the proper gap.
Setting pickups too high can cause a number of unusual occurrences. Depress strings at last fret. Using a 6″ (150 mm) ruler, measure the distance from the bottom of the first and fourth strings to top of the pole piece. A good rule of thumb is that the distance should be greatest at the fourth-string neck pickup position and closest at the first-string bridge pickup position. Follow the measurement guidelines from the chart below as starting points. The distance will vary according to the amount of magnetic pull from the pickup.