On the upper frets of my E and B strings i am experiencing notes that sound way out of phase. Is there something that can be done to avoid this or is this just the nature of E and B strings in general and I should learn to just deal with it?
Well, a note can not really be out of phase with itself, but weird things can happen. I suspect your pickup is too close to these strings, causing the strings to be excessively pulled by the pickup's magnet.
When playing on the high frets the thicker strings are too massive/stiff for their (fretted) length to vibrate and produce all of the harmonic series correctly. That's why a D on the 10th fret of the E string sounds different than D of the 5th fret of the A and different from the open D. Lighter gauge strings can help but I would just find a different place on the neck to get the notes you need.
Geoff: It sounds almost like a chorus effect I guess it is just the nature of the instrument. It really isnt that big of a deal, I mean, how often do most of us find ourselves wanting to use the 17th fret on the B string anyway? But either way it is difficult to intonate the B string because the pitch wavers when I play the 12th fret.
It sounds like you might have a bad string. Have you replaced the strings and still have the same problem?
While a choked sound is sometimes related to thick strings over a short distance, as Greg mentioned, the description of "chorus effect" makes me think that it's the other possibility: pickup too high, and magnetically attracting the string when fretted down. I'd try lowering the pickup.
+1. The ''chorussy' sound youre getting might be the result of the pickup pulling on the string as a note is fretted, causing it to subtly shift pitch. (This makes sense if it's worse on the higher notes, as the higher you play, the closer the strings hit the pickup) Try to lower your pickup, that should prolly help.
I hade this same problem with my SX bass when I put new pickups on it.. Everything after the 12th fret on the D & G string had a chorusing sound. I dropped the pickups and it went away.