AIUI, git pull remotename branchname is exactly equivalent to git fetch remotename ; git merge remotes/remotename/branchname. Too, I'm pretty sure Git updates the branch pointers under remotes/ every time it talks to the remote in question, although if this isn't happening for some reason, it'd explain why it thinks you are behind the upstream branch you just pulled from.

Is this happening on your Dreamhack, by chance? If so, d'you mind if I take a look at your git repository there and see if I can figure out what's going on?