In DejaOffice>Settings>Logging and Support Settings>Record Counts it shows:
DejaOffice Record Counts:
DejaContacts: 4530
DejaCalander: 413
..
Native Record Counts:
Native Contacts: 9089
Native Calendar: 0

Why dont the DejaContacts record count match the Native Contacts count?

When I sync using CompanionLink, it gives the correct record counts that matched DejaContacts = 4530 and DejaCalander=413, so it is syncing correctly.
My environment:
PC with Outlook 2013 and CompanionLink build 6042
Samsung Galaxy S3 with Android 4.4.2

In Sync Settings:
Sync with Android Contacts App checked
Contact Account=DejaOffice
Sync with Android Calendar App checked
Calendar Account=My calendar

Under Contacts on the Phone:
When Contacts to display=DejaOffice only, is shows duplicate records.
When Contacts to display=All Contacts only, is shows duplicate records.
When Contacts to display=Phone only, is shows no records.