I would understand logging in as a reputation boost if staying logged in and visiting the site also did the reputation boost. It seems that it only kicks in if you explicitly log in.
Yeah, that's a bug that I noticed last night. The board software doesn't trigger the login event unless you explicitly log in.. so I'm going to adapt it to work like you describe. What will most likely happen is that we roll out ways to boost your rep a few at a time and watch the system for a few days so we don't have some ways that are too overpowered.
My first concern will be reintroducing weighted up/down votes.. where a person with a higher rating can make a bigger impact. I think it's capped at +8 max and -4 min at the moment.