As anyone would expect AD administration is not the same as CROWD and changing things in AD is almost always a very bureaucratic process that takes many days.

Duplicate groups should only give warnings and not stopping the synctronization. In addition to that, the number of groups with duplicate names cannot be detected at once... so if you have 100 duplicates and it takes 7 days (optimistic) to solve a duplicate group naming issue in corporate Active Directory, it could easily take years to setup Crowd.

012-03-23 15:03:05,013 scheduler_Worker-0 INFO [atlassian.crowd.directory.DbCachingRemoteChangeOperations] scanned and compared [ 13533 ] groups for update in DB cache in [ 356ms ]
2012-03-23 15:03:05,051 scheduler_Worker-0 INFO [atlassian.crowd.directory.DirectoryCacheImplUsingChangeOperations] synchronized [ 13533 ] groups in [ 394ms ]
2012-03-23 15:03:05,414 scheduler_Worker-0 INFO [atlassian.crowd.directory.DbCachingRemoteChangeOperations] scanned and compared [ 13533 ] groups for delete in DB cache in [ 363ms ]
2012-03-23 15:03:05,453 scheduler_Worker-0 INFO [atlassian.crowd.directory.DbCachingRemoteDirectory] failed synchronisation complete in [ 23868ms ]
2012-03-23 15:03:05,467 scheduler_Worker-0 ERROR [atlassian.crowd.directory.DbCachingDirectoryPoller] Error occurred while refreshing the cache for directory [ 32770 ].
com.atlassian.crowd.exception.OperationFailedException: Unable to synchronise directory: duplicate groups with name '#SE - EMEA'
at com.atlassian.crowd.directory.ldap.cache.AbstractCacheRefresher.synchroniseMemberships(AbstractCacheRefresher.java:133)
at com.atlassian.crowd.directory.ldap.cache.AbstractCacheRefresher.synchroniseAll(AbstractCacheRefresher.java:44)
at com.atlassian.crowd.directory.ldap.cache.UsnChangedCacheRefresher.synchroniseAll(UsnChangedCacheRefresher.java:223)
at com.atlassian.crowd.directory.DbCachingRemoteDirectory.synchroniseCache(DbCachingRemoteDirectory.java:621)
at com.atlassian.crowd.manager.directory.DirectorySynchroniserImpl.synchronise(DirectorySynchroniserImpl.java:63)
at com.atlassian.crowd.directory.DbCachingDirectoryPoller.pollChanges(DbCachingDirectoryPoller.java:50)
at com.atlassian.crowd.manager.directory.monitor.poller.DirectoryPollerJobBean.executeInternal(DirectoryPollerJobBean.java:29)
at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:203)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:520)