At the current stage of the connector I think it would take a lot of work to make it work with multiple forums based on these reasons:
1) Currently their is 1 field in the comprofiler table which indicates the CB user's forum id... would need multiple fields
2) Currently the connector loads the phpbb config and common files so that it can use phpbb's own functions to handle some of the tasks like login/logout, etc... with this happening the multiple config files would conflict with each other...