Took my PRS/BM to Guitar center to get the bridge adjusted and a new set of Elixers installed..For 40 U.S they cleaned the frets, polished it etc...When I got it home it played GREAT! but when I put it on the tuner on my Valvetonix an tuned it, the top E string when fretted at 5th fret and the A string open, the A string was flat..or the E string was sharp.. From A on down doing fret tuning it was on the mark. What gives?

Appreciate any help