It sounds like it could well be intonation. Heres how to check:
1) tune your guitar with a good electronic tuner. Tune the strings from low to high until they are all spot on.
2) play your open note and then fret the octave on the 12th fret.

The fretted note should be exactly an octave above the open note and if your tuner is any good it will tell you if the fretted note is on or not.

If it is well good if not you will have to either fix the intonation your self by adjusting scale length (by moving the saddle either closer to the nut or further away, this will require a small screw driver)
or
get a tech to do it. It is not a difficult thing to do but if you are unsure, get it sorted out professionally.
gluck !