Don't purposely come back to a break late, but if you do happen to come back a bit late don't panic about the timer starting again. I was waiting in line to sign back in to get in for the verbal section the first time I took the MCAT and got there a minute or two late and saw the screen change to the verbal instructions and the timer never started. I freak out and ended up not doing well that sitting but, moral of the story - stay calm, be on time, use your break, be confident.