Red Hat Directory Server, LDAP paged search results are not always returning all records

Solution In Progress - Updated -

Issue

I have an application that imports users from Red Hat Directory Server, and it uses pagedResultsControl in search.
The server does not return all the records to the application, a few thousands entries are not listed.
But the correct number of entries is returned by a similar ldapsearch command.

Environment

Red Hat Entenprise Linux 6
Red Hat Directory Server 9

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