there is probably a problem with the intonation of the high e saddle OR there could be a kink on the string. try doing an intonation test by comparing the high e harmonic with the fretted 12th fret e note, this should tell you if your saddle needs to be moved forward or backwards. to check for kinks, look at the string and see if there are visible signs of bending along the vibrating area of the string itself (between the nut and the bridge). kinks along the string and debris from wiping cloths can get stuck on the string dampening vibrations when you play.
also try adjusting the height of the pups to see if this improves the output volume of the plucked string. but be careful magnet pickups have an optimum distance that they should be at from the string, otherwise, the magents hinder proper vibration of the string and messes with how you can tell if your guitar is properly intonated and tuned.
