I'm a new (new to LC fanfic, anyway) writer who's been studying writing at conferences and in books and magazines for a few years, and you're describing something that apparently ALL writers experience. I wish I knew exactly what it was or how to control it. I could bottle it, sell it, and retire on the royalties from just the first-year renewals. Sheesh! I've had characters do and say things that I never intended. I've had people jump in who were supposed to be cardboard cutouts in the background and demand to be taken seriously. I've even had intended main characters just disappear from the story altogether, and that's extremely frustrating to me, since I'm one of those 'organize the organization' types.
I'm just glad that I'm not the only psycho out there who sees his/her characters take over and go boldly where no word processor has ever gone before.
