Gearhed, this could be a dozen different things. If this happens as you go up the neck that the picthes aren't in tune, then you likely need your intonation reset on your bridge. Not a hard or expensive process, but it requires very very precise tools; something you'd want to get done at a shop. If you can actually hear the strings GOING out of tune as you go up the neck or as you vibrate, then you just need to restring the guitar. Something like that is often the result of too many or too few wraps around the tuning peg, or just strings that haven't stretched yet.
There's an easy way to check if a fret is off. Just get your tuner and go across all 6 strings at that fret, e.g. the 14th. Play your low E at the 14th fret. Watch the tuner, but don't tune the string. Play your A at the 14th fret. Watch the tuner. Do this across all strings at that fret and try to watch and see if there is a noticeable shift across the strings. Are they all off by about the same amount? Does it gradually get flatter or sharper going toward either side of the neck? Sort of a poor man's way of measuring.
It could also depend on how you have your neck set up. When was the last time you took the guitar into a shop? Could it be that the truss rod hasn't been adjusted recently? If it played in tune before, but isn't playing as well in tune, then this is just a problem with the setup, which would include bridge and neck adjustments. Also, if you play with a lot of relief in your neck, it WILL go out of tune as you go up the neck by some amount.
That's what I can come up with as possibilities that could fit your description of symptoms. Let me know how that helps!
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