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missing users in groups in alfresco 5.0.b

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I have upgraded to 5.0.b from 4.2.f community. Most of my groups are now empty in alfresco. It seems like it is not synchronising fully.

I have used the following config for all previous version of alfressco community since 3.4.d

### AD SSO
authentication.chain=passthru1:passthru,ldap1:ldap-ad
alfresco.authentication.authenticateCIFS=false
ntlm.authentication.sso.enabled=true
passthru.authentication.authenticateCIFS=true
ldap.authentication.active=false
ldap.synchronization.active=true
ldap.authentication.userNameFormat=%s
ldap.authentication.allowGuestLogin=false
ldap.authentication.escapeCommasInBind=false
ldap.authentication.escapeCommasInUid=false
ldap.authentication.java.naming.security.authentication=simple
ldap.authentication.java.naming.factory.initial=com.sun.jndi.ldap.LdapCtxFactory
ldap.authentication.java.naming.provider.url=ldap://echo.uk.domain.com:389
ldap.synchronization.java.naming.security.authenticaton=simple
ldap.synchronization.java.naming.security.principal=administrator@domain.com
ldap.synchronization.java.naming.security.credentials=***
ldap.synchronization.userSearchBase=ou\=Sites,dc\=domain,dc\=com
synchronization.synchronizeChangesOnly=false
### synchronization.import.cron=000**?
synchronization.syncWhenMissingPeopleLogIn=true
synchronization.autoCreatePeopleOnLogin=true
passthru.authentication.domain=DOMAIN
passthru.authentication.servers=DOMAIN\\echo.uk.domain.com,DOMAIN\\jarvis.usa.domain.com
passthru.authentication.defaultAdministratorUserNames=johnl,markw,administrator,alfresco,sharifu 
ldap.synchronization.queryBatchSize=1000
#ldap.synchronization.groupDifferentialQuery=(&(objectclass=nogroup)(!(modifyTimestamp<\={0})))
#ldap.synchronization.personQuery=(&(objectclass=user)(userAccountControl\:1.2.840.113556.1.4.803\:\=512))
#ldap.synchronization.personDifferentialQuery=(&(objectclass=user)(!(modifyTimestamp<\={0})))
ldap.synchronization.groupQuery=(objectclass\=group) 
ldap.synchronization.groupSearchBase=cn\=users,dc\=domain,dc\=com 
# Delay indexing to improve replication performance
#index.tracking.disableInTransactionIndexing=true
#lucene.maxAtomicTransformationTime=0
5.0.b


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