Also, when you're beginning to play it's hard to distinguish the difference between pitch and tone... Pitch is most commonly what defines a string to be "in tune" However, the TONE is something completely different. You'll notice that each string is a different guage (thickness)... this is what gives the strings their individual tone. This is most easily demonstrated by the way the E string sounds compared to the e string (E being the 1st and largest string and the e being the 6th and smallest). It might be that your ear is compensating for the deeper and tricking you into thinking that you need to tune the string higher than it needs to be...... This is just a suggestion of what might be happening... I suggest getting an electronic tuner at a local guitar shop that will give you a read out of the strings rather than you having to do it by ear... This will help you store a representation of what it SHOULD sound like in your mind that way you'll be able to train your ear a lot faster...
I had trouble tuning by ear when I started and the whole tone/pitch thing was what I found to be the problem for me... I am fine and dandy now 6 years later though. haha.
