I'm not sure if this is a common problem so sorry if I could find the answer elsewhere. Something is weird with the the low e string on my guitar. When I play the string open, it is in tune with the 12th fret and the 12th fret harmonic, but when I play the first 5 frets(F-A), the notes are a little sharp. How do I fix this?
Yeah it's perfectly in tune with the 12th fret and the 12th fret harmonic. Seeing as I'm not a expert on setting up guitar I figured I would ask people to make sure I'm not doing anything stupid =D
I would take it to a really experienced tech/ luthier. He'll be able to get your guitar as close to perfect as possible. You've got to remember however, that the notes on a guitar are never going to be perfectly in tune, its an imperfect instrument.

Another cause of the sharp notes could be you, you may be pressing down a little to hard on the strings causing them to go sharp.
"Swords, nature's hell sticks."- Trip Fisk