I have done quilting on my janome 6600 also.
The usual suspects if it is not turing out right..not threaded right, tension,going faster or slower than the machine..i had some tension issues the other day, and i took it all out, and stitched in the ditch. i just wasn't in the mood to fool with her..
what Janome do you have? there are message boards for janomes..i belong to the 6500/6600 yahoo board.