I've had a similar issue. I can add a user to a group, and when I look again they show as belonging to the group, but they do not appear to have the appropriate permissions. That is, though userA is a member of GroupA, he cannot access an I-Bay that for which access is restricted to GroupA.
FYI I run a supported version of the SME 5.5. and Mitel is looking into it.
Robert