It is suggested
here on the Virgin website, that you check in 2 -3 hours before your flight.
I have seen other reports that BOS ground staff struggle to cope when the weather is bad and the loads are high. To defend them slightly, there must be an awful lot happening and it may be a case of right hand / left hand.
Glad you got to experience UC, despite the poor way you were treated. Often the reluctance to upgrade to UC is because of catering issues. Just because there are empty seats, it doesn't mean that there will be enough food if they fill them.
Nick