You should check Intonation. There must have some old thread about this here, somewhere.
Using new strings, check 5th position tunning. As it is raised, you must move its saddle towards the neck. Tune the open strings, check again and move the saddles until the 5th position looks right.
Then, you must check further... Do all this on frets above 12th position until reach 24th fret.
The tip is:
- If the Note seems raised, move saddle towards the Neck.
- If the Note seems sharpened, move the saddle towards the Bridge.
Use your ears and remind that Harmonics can be very helpfull when adjusting Intonation (since you keep all strings perfectly in tune again all time you've changed something).