After creating a directory, importing users from a provider does not include group memberships on the first attempt.
If the import is attempted again, group memberships are added.

Import from JIRA:

2009-10-20 14:41:12,646 http-8095-3 INFO [crowd.importer.importers.BaseImporter] Importing 10 groups.
2009-10-20 14:41:13,215 http-8095-3 INFO [crowd.importer.importers.BaseImporter] Importing 2653 users.
2009-10-20 14:41:23,399 http-8095-3 INFO [crowd.importer.importers.BaseImporter] Importing 2766 group memberships.

2009-10-20 14:41:23,407 http-8095-3 ERROR [crowd.importer.importers.BaseImporter] Could not add memberships for group 'jira-administrators' as it does not exist in directory with ID: 557057
com.atlassian.crowd.integration.exception.ObjectNotFoundException: Failed to find entity of type [com.atlassian.crowd.integration.model.group.InternalGroup] with identifier [name <jira-administrators>, directoryId <557057>]
at com.atlassian.crowd.model.group.GroupDAOHibernate.findByName(GroupDAOHibernate.java:52)
at com.atlassian.crowd.integration.directory.internal.InternalDirectory.findGroupByName(InternalDirectory.java:561)
at com.atlassian.crowd.manager.directory.DirectoryManagerGeneric.findGroupByName(DirectoryManagerGeneric.java:379)
at com.atlassian.crowd.manager.directory.DirectoryManagerGeneric.addAllUsersToGroup(DirectoryManagerGeneric.java:1185)
.... repeat for all 10 groups

Now try the import again to the same directory -

2009-10-20 14:45:37,454 http-8095-3 INFO [crowd.importer.importers.BaseImporter] Importing 10 groups.
2009-10-20 14:45:37,457 http-8095-3 INFO [crowd.manager.directory.DirectoryManagerGeneric] Group <com.atlassian.crowd.integration.model.group.GroupTemplate@7bceb29e[name=Accounting,directoryId=557057,active=true,type=GROUP,description=Accounting]> already exists in directory. Skipping over this entity.
.... repeat for all 10 groups
2009-10-20 14:45:37,698 http-8095-3 INFO [crowd.importer.importers.BaseImporter] Importing 2653 users.
2009-10-20 14:46:11,037 http-8095-3 INFO [crowd.manager.directory.DirectoryManagerGeneric] User <com.atlassian.crowd.integration.model.user.UserTemplateWithCredentialAndAttributes@32f12531[name=john citizen,directoryId=557057,active=true,emailAddress=user@domain.com,firstName=John,lastName=Citizen,displayName=John Citizen,iconLocation=<null>]> already exists in directory. Skipping over this entity.
.... repeat for all 2653 users
2009-10-20 14:46:11,050 http-8095-3 INFO [crowd.importer.importers.BaseImporter] Importing 2766 group memberships.