Why is this happening?

[DrumsFoDaSoul]

Are you using the Kyser quick capo or whatever? If so, those things are not very good. Get a real capo that's not one of those "quick change" kinds and your problem should be solved.

no, i'm not. i use this:

ftp://ftp.sonic.net/pub/users/shubb/S1_300.jpg

Those are nice.

[Kahn]

very nice

[zenful]

what is intonation exactly?

i think it has something to do w/ distances between the 12th fret and your bridge and the nut.

from wikipedia so i might be wrong
Intonation, in music, is a player's realization of pitch accuracy in music to oneself and across an ensemble. If musicians have "bad intonation", it means they play or sing out of tune. Intonation can also mean tuning.
[edit]

Strings

In string instruments, intontation is more of a worry than in other instruments. Because most string instruments are unfretted, if a finger is too high or too low by even a fraction of an inch, the note will be out of tune. The process of gaining good intonation typically takes many years of playing to acquire and is arguably the hardest part of learning a stringed instrument.

this isn't referring to intonation of a guitar; this is referring to someone who plays violin or cello

intonation of a guitar has to do with the gutiar's ability to stay in tune on all six strings as you go up and down the neck. unlike a violin though, a guitar's intonation cannot be changed while playing: it's semi-permanent.

there are lots of factors that could affect a guitar's intonation: straightness of neck, fret wear, and even the age of the strings

the truth is, putting a capo on any guitar will cause it to go out of tune, even if only by the slightest bit (and it gets worse as you go farther up the neck)

[whatshername]

so i just got back from burlington guitar and amp. they had their martin specialist check it and he said it's just that the action is too high. and the moisture in the storage unit could have caused it. it's gonna cost 15-20 bucks to get it fixed. the storage place will be paying for it. bitches.

[ericwormann]

You (meaning "anyone") should get your guitar set up once a year if you play it regularly. A set up can be anywhere from $20 to $50 depending on where you go. Basically they check the intonation, clean the frets, probably throw a new set of strings on there, adjust the action, check your truss rod, etc. Just basic maintenance stuff. Think of it as getting your oil and filters changed.

Also, intonation is how accurate the length of your strings are from bridge to nut. If you look on strat-style electrics, there are little screws with springs around them to adjust the saddles on the bridge. This changes the distance from the saddle to the nut. If it's off a little bit, then the guitar will sound in tune when the string is open but will be out of tune when it's fretted. The basic rule of thumb is that the 12th fret is the half way point. (the distance from nut to 12th fret = 12th fret to bridge) If your intonation is a little off, then (for example) an A note will sound a little bit higher or a little bit lower than what an A note is supposed to sound like.

[i-am-me]

i thought i had that same problem a while ago with my high E string. turned out i needed a new set of strings. haha