This can happen because with 9.1 we changed the way we read the users form a group. This is done now with one search query with a filter over the groupMembership attribute.
To fix this you need either a new version of eDirectory (at least 9.1.1) or add an index to the groupMembership attribute.
An index is anyway a good Idea to speed up the synch performance if you have set an ImportUsersOfGroup.
eDirectory Bug which causes this problem and was fixed with eDirectory 9.1.1:
LDAP paging returns the same values for each page (Bug 1071840)