I think there are some other interesting facts for a ticket that might help as mentioned in some other thread and some are random guesses:
Had all of the members a champion regalia when grouping dominion? Had they a champion regalia before patch 5.0.2?
How many groups at the same time could be send in (for the guilds i heared there could only be send 3 groups, instead of 6 before patch 5.0.2, the others couldnt queue...)?
For any reason, had all group members the same pvp (flag) status before tagging dominion (on or off)?
Had your guild set any rubies in the new ruby tree?
These could be some hints what went wrong, i dont know, perhaps some of this might help solve this problem -.-