Communication lost - Same installation, same version of client (.exe), but client has different configuration in Configuration Manager properties

Question

Hi, I can't understand how I get the following different between old and newly installed client. On the left side it is the original client configuration and on the right side it is what client gets after installing the same version of CCMSETUP.EXE (5.00.7958.1000)
with SCCM 2012 R2.
Differences noticed:
-Catalog's name (in Software center) are different. New client has "IT Ogarnization" as name for their catalog.
-Configuration Manager Properties for new client doesn't have "Configurations" Tab.
-Many Components status in the components tab are different: CCM Notification Agent, Compliance and Settings Managment, Hardware Inventory Agent, Out of Band Mangement Agent...
With all this, I can't send Windows updates or any applications to ANY clients. The client status in the monitoring deployment always shows "Unknown". 
I don't think it is on the client side, because I return to older VMware snapshot and see the different, after uninstalled and re-installed the SCCM agent, I get the new "problematic" client configuration.
Any suggestion to resolve my problem? Thank you in advance.
bsuperkid

Answer 1

Here the all three logs. Sorry to give them like that but I think it is best way to let you take a look. I did change some name and reference to hide my environment. 
Also, I don't know if there a link with my problem, but I guess so.
- I noticed in Monitoring\System Status\Components Status\"Warning SMS_WSUS_SYNC_MANAGER", the following message (ID 6703):
WSUS Synchronization failed.
Message: Thread was being aborted.
Source:
Microsoft.SystemsManagementServer.SoftwareUpdatesManagement.WsusSyncAction.WSyncAction.SyncWSUS.
- I noticed in Monitoring\System Status\Components Status\ "Warning SMS_AD_SYSTEM_DISCOVERY_AGENT", the following message (ID 5203):
Active Directory System Discovery Agent reported errors for 2074 objects. DDRs were generated for 0 objects that had errors while reading non-critical properties. DDRs were not generated for 2074 objects that had errors while reading
critical properties.
Possible cause: The site server might not have access to some properties of this object. The container specified might not have the properties available.
Solution: Please verify the Active Directory schema for properties that are not replicated or locked.
Refer to the discovery logs for more information.
I'll upload a print screen of all three logs files. If you need it in text format, I'll upload them as the code Block.
Thank you again!
bsuperkid