I think a simple checkmark to the right of the username would work. No need to wrap it in a rounded box, IMO. Also, slightly darkening the background color of processed rows might help (why is the whole so grey in the first place, btw?)
I just pushed an update that added the show/hide markers and changed the categorization marks to look more like the buttons and tabs (without being 3d and therefor, hopefully not looking like a clickable button).
Well, when one first opens the tool, all users are collapsed. Shouldn't the first one be selected then? (Although I'd prefer the alternative: having the ability to collapse the users to get an easier overview at the user list).
Why does one user have to be selected at all times? It shouldn't be hard to do a simple check for that and prevent actions that require a target user (assuming that's the problem).