Is the reference you have a six character code, a mixture of letters and numbers?
Group bookings have a number of unique features in a reservation system. Because of the nature of the contract between the airline and the operator they don't want individual passengers calling and changing flights (that's not what you want to do but...). Thus all comunication should go via the agency/operator. What will usually happen is that the airline will assign all the seats in a block although special requests can be entered in the booking by the operator (but are not guaranteed). But not all operators are totally switched on or copoperative.
Then there is the issue of locking and unlocking the booking. It's possible for 2 terminals to LOOK at the same booking simultaneously but only 1 can update it. With a normal booking (9 or less people) there is some risk of two people trying to checkin separately but I suspect it is considered manageable because 1 will get a try again in a minute. A group can be 99 (or more, depends on the booking system) which could cause more problems. Once you get to the airport you are no longer in reservations but departure control which is a different kettle of fish.