Oh well, it was a shot, because I had exactly the same problem when I started using later versions of FlashGet. Next OS install, I go back to older FlashGet versions. v3.x sucks.
Prooobaaa - Do you have a recent version of FlashGet installed, that might be stealing your associations? Recent versions have a BT client built-in, and it steals .torrent associations by default.
If you're downloading it manually, it's not an installer; it's meant to simply replace your utorrent.exe file wherever you have it installed. It can't be running at the time, of course.
You did misunderstand. He was talking about seeding until at least one person has a full copy. Apparently, that now takes about 135% when using superseed.