I imagine there are a few folks who feel as I do when it comes to hearing my recorded voice. We don't like to hear it. Rather like those actors who don't care to see themselves on screen. To me it's fantasy versus reality. In my body, my voice resonates so beautifully and it's a joy to step outside oneself and hear it. Then I hear it recorded and I just want to duck and cover. I hear every little thing and I think OMG that's what I really sound like? It's discouraging, I agree. Especially when it's a live recording and no opportunity to punch back in. The beauty of live performance on the other hand is that it is fleeting, with no rewind, and combined with all the other elements that go along with a live performance, location, ambiance, the other players, the energy of the audience, etc, a rough spot goes by scarily noticed because it all flows together so seamlessly. Auto tune is for those folks who can't sing consistently in tune OR who are relying on looks rather than substance… i.e. the Brittany Spears of the world whose vocals are so electronically augmented one can scarecly distinguish what is really her and what isn't. So many of the artists of today are being manufactured to appeal to the pop culture based mostly on appearance rather than capabilities. Guess that's why they build hugh shows, with back-up dancers to divert attention away from lack luster vocals. Just sayin'…

To be honest I am a big enemy of auto-tune. I can always tell when it has been used in recordings and I can't help but feel disgust at how unnatural it feels. Also I feel that just like soccer players get paid millions to be superhuman, so should a famous singer be able to perform at the very least correctly. Do not get me wrong, I am all for technology and I do not want to troll this forum, but auto-tune is like using steroids for muscle building, and it should only be used as a premeditated effect, or when there is really no other choice (i.e. the bad fragment cannot be re-recorded). One must remember subtlety is your ally in studio, as opposed to live where you often need power and feel.
Having said that, next time you see yourself missing a note often in studio, ask them to regulate the reverb on your monitor (headphones) so that you can get a good enough feedback and can comfortably sing in tune. The super-muffled studio booths for singers offer less echo than usual and it can be hard to sing at ease.
Other reasons affecting a part where you are out of tune might be vocalization: try to shape your mouth with precision in a more exaggerated way than usual.
I hope I did not sound patronizing since I just want to be helpful.
Keep it up!