Have you tried replacing just that string to see if it helps? String could have went bum.
Heres a couple inspections to help find the problem:
Take a loot at the frets and ensure they are seated flat on the fretboard, the outsides are usually where they start to pop out if they weren't radiused before installation.
Inspect the nut. Press down on the 3rd fret area and ensure the string isnt touching the first fret after the nut (which would mean the nut slot is too low)
Make sure your truss rod is properly adjusted (there are plenty if instructionals on the web.)
Check the neck angle with a 24" straight edge. - Adjust truss rod to make neck dead straight and lay the straight edge on the frets and slide it toward the bridge. The straight edge should lye flat on the bridge (if its an acoustic) NOT the string saddle or significantly below it. If its an electric, use good judgement depending on the type of bridge you have, it should relate close to the above instructions for an acoustic.