I think most of you are too harsh on the OP. If there is still a check-in line, I expect an airline to check in a passenger even if he is "late" (assuming that we are talking about the 60-min-before-departure deadline). I regularly arrive only 55 mins before departure in Dubai, and i have never been denied my BP.
Charging USD 400 for rebooking the outbound and NOT making sure that the return flight is rebooked is clearly the airline's fault. Most occasional travellers do not even know about the cancellation rule.