Full green doesn't mean full rep. Put your mouse over the rep to see what the rank is. You can find a list of the ranks in a sticky thread at the top of this section.
As for the reps going away when a thread is removed or not going away when someone is banned, I'm not sure how that would be fixed. It would be nice to see the rep system get a major overhaul, like more bars or add stars or something like that, but it's been brought up in the staff section multiple times and it comes down to it being very complicated and difficult to get done.