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Discovery What are The OU’s Targeted? In AD Are they missing any in OU’s IN AD ??
From AD In above Ou’s Howmany Computers are there? (From AD) may be a difference in SCCM vs AD
in SCCM Now List howmany in SCCM may be a difference in SCCM vs AD
Run the AD stale Computers Command  Use this link http://configmgr2oo7.blogspot.sg/2010/09/for-finding-90-days-old-computers-in-ad.html Computers that are not connected in network or not logged on more than 90 means
 computer not there in network and SCCM treats as Stale and it will not discover
Get the difference of computers(AD-StaleAD-in Totall SCCM) Totall??  
Now get the Totall non SCCM Clients show in your clients report and fix by using below two tools    
Use these script to install the SCCM Client on remote computers    
                   -remotly install on many systems once by using these scripts http://configmgr2oo7.blogspot.sg/2009/01/sccm-client-installation-script-batch.html
http://sccmcat.codeplex.com/
USE SCCM Client action tools ..need to configure the .ini file as per your requirement check the blog
                  – Single computer based tool http://sourceforge.net/projects/smsclictr/ If it is a one computer use this tool
Catagorise the problems lile Ping Online & offline computers with this script to get the status of computes use this scrip may be usefull before you start work
WMI & Admin$ issues http://configmgr2oo7.blogspot.sg/2008/11/wmi-connectivity-check.html WMI & Admin$ is key to deploy clients
Once the clinet installation completed check the log CCMsetup.log,execmgr.log, Clientidmanager.log check the logs
  Check all these case’s before start working http://configmgr2oo7.blogspot.sg/2010/03/client-troublshooting-checks-check-list.html  
 

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