Help! Weird Kitten Behavior

My new 6 week old kitten has been using his litter box perfectly for the past week.
Today, he jumped up from sleeping on my lap and went into the dining room to potty on the carpet. He tried to cover it and I immediately picked him up and put him in his litter box.
He jumped out of the litter box and scampered off. I proceeded to clean up the carpet, and went to look for him about 5 minutes later.
He was hiding under the bed but had pooped in the corner of the bedroom minutes after having just been in his litter box!
He has never done this before, so I am so confused. He has been using his litter box without fail before this episode.
Any suggestions?

something must be bothering him about the litter box. The type of litter? Is it private? Is it hard to get to? Did a loud noise scare him while he used it? Clean it thouroughly and replace with fresh litter and see if that helps. Or try moving it somewhere else. Sometimes they get really picky about clean litter.
He's still a tiny little baby. Maybe he's just confused.

wow, 6 weeks only? where did you get such a young one? was he orphaned?

Anyways he is REALLY young, he may be a little off on his habits and behaviors since he was seperated from his mother at way too young of an age. Be patient, also be aware of some of the issues kittens like yours can have as they grow up. Confine him to a small room or crate when you are away, I hope he doesn't just have free run of your entire home. It is just too big for such a small kitten. They can forget where to go or not be able to make it all the way to the box in time.

Maybe he wants two boxes (ya know one for each...um function). He is awfully little. Is he the only cat? I'm thinking the little chap might be confused, and there's no one to ask directions...

He could be sick. Mine only went out of her box when she was so ill that she couldn't control herself. Have you had him checked out by vet to make sure he has no worms or parasites?