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Have to run slapindex twice

I start by loading my LDAP database with ldapadd or slapadd.  Start slapd and all information imported is available.  If I stop slapd and do a slapindex and then restart slapd, some of my LDAP information is not available.  In some cases entire branches are missing.  If I stop slapd again and run slapindex for the second time, all my information is available again.  Am I doing something wrong?  Is my version of DB not old enough.

Linux Red Hat 7.3
OpenLDAP 2.0.25

>From slapd.conf
index uid,cn,gidNumber,uidNumber,memberUid eq
index objectClass pres,eq