Say am playing this

E -----------------5---7
B ----------------3---5
G ----------------
D ----------------
A ----------------
E ----------------

The sound is meant to sound nice and the notes are meant to compliment each other. However on my guitar the notes dont compliment each other and just dont sound right. Is it most likely an intonation prob?
OK, here's how to check if you have an intonation problem, play the 12th fret (natural) harmonic and then play 12th fret fretted down. If there's a difference you may have an intonation problem.
press the 5 on the E string and see if its tuned as an A to make sure its tuned on that fret. Ive never had an intonation issue that low down the neck, though
'I love her, but I love to fish...I'm gonna miss her"
I have a similar situation that I need help with. On a couple of inexpensive chinese made guitars, I can almost get the 12th fret to agree with the open string, but every intervening fret is sharp. So an open chord, like a D or E is dischordant. It's like the nut is in the wrong place or the first fret should be closer to the nut. any way to adjust my way out of this problem? Patrick