I have tried to search the forums and PITs and do not see anything on this so please excuse me if I am adding a duplicate suggestion. I did submit this as a suggestion on PIT too.
The rendering of checkboxes when using two or three column is less than ideal. It renders the checkboxes inline separating the rows by a <br /> tag. This makes it harder than it needs to be to line up each columns checkboxes instead of letting them stagger as they currently do.
I would suggest rendering each "column" of checkboxes into a wrapper class that designers can easily style to their liking in order to set custom margins and line-height.