#1
So recently i noticed that although i've intonated my guitar when i fret the note its still slightly sharp. This occurs on all fret positions and strings except the high E. Any thoughts on why this is?
#2
physics...

fretting a note causes it to sharp just like bending a note would, although its generally negligible. taller frets will sharp more than shorter frets.
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#5
Couple reasons it could be. High action is one since you have to bend the string farther. Another is that the bridge isn't in the right position. Guitar strings don't vibrate perfectly with each other so each string normally requires a slightly different scale length, which is why tune-o-matic bridges are out there and why a lot of acoustic bridges are curved.

In addition, guitar frets are close approximations of where a note is across all the strings. It isn't actually where the note is. There are guitars that have frets for every note on every string to fix this problem and they look crazy. So you may just be running into a case where it is a decent amount off on some parts of your guitar.

The final reason I can think of is that your guitar may just have been badly fretted. I had a crappy guitar that didn't have the right spacing of frets for its scale length, so the higher you went, the more out of tune it got.

Those are some ideas and it's probably one of the ones in the top paragraph, I just figured you might as well know some other reasons in case lowering the action or adjusting the bridge didn't fix it.