Gah, they really are two different systems ;)

Everyone's votes count equally as +1/-1, there is no commenting, and they don't affect a user's reputation.

Giving reputation is when you comment on a post to affect a poster's reputation based on your own reputation.

Thats how it is on another VBB site im on also :)

Oh, really? What site? This was a system that I built myself, and wasn't aware that it had ever been done before. I'm curious to see how another site implemented it.