Hi Tyoud, Thanks for posting all the logs, it makes it easier to give a correct answer the first time.
The logs show you have 2 problems, perhaps related.
First, your SEPM database has some corruption which needs to be fixed before moving forward. In this state your Manager most likely cannot communicate properly with any of it's clients. When you upgrade your server to a newer SEPM server, there are tools that run during the upgrade process that fix known database issues that previous versions, such as MR2, can cause. So here is what I suggest you do.
1) Upgrade to the latest version of SEPM -- RU5 was just released.
2) After you upgrade, open a command prompt and navigate to the SEPM install directory.
3) You'll see a subdirectory called "Tools", open that.
4) Run the file, DBValidator.bat
If this says there are NO errors, then check the scm-server-0.log file. If there are no "Broken Content Link" errors then the problem has been resolved.
If the DBValidator BAT says there is still an error, or you still have the "Broken Content Link" errors, open a support case. Tell them you have a corrupt database. The database file itself isn't physically corrupt, but some of the data inside is not valid.
If you don't want to migrate this machine (producting environment) then export the database and import it into a test machine and try the upgrade there. If you absolutely must have this machine fixed before you upgrade, then open a support case and be ready to give Support a backup of the database. Sometimes they will give you a tool to fix just your DB
I really suggest migrating the server to RU5, it will probably be a lot faster than calling support. If it fixes the problem, your done! (and you have an updated server). If not, you'll have to call support anyways.
Now before you address the second issue, first address the first issue. The second issue may be related to the first, and you even if you fix the second issue, you really can't do anything until the first issue has been addressed.
The second issue is that the client is rejecting the servers communication because the policy files have not been signed correctly. This is because there is a certificate mis-match between the SEPM server and the client. The index file itself is not bad, but the client cannot verify it came from the correct source.
This may happen if you un-install and re-install the SEPM server. It may also happen if run the Configuration Wizard multiple times. We are trying to prevent these issues from happening in the next major version of SEPM.
The client stores a certificate in the file called Sylink.xml. If this certificate does not match the servers certificate, the client rejects the servers communication. This is a security feature to prevent man-in-the-middle type attacks.
To correct this issue you can either:
1) Manually copy an updated sylink.xml file onto all your clients client.
See this KB article:
http://service1.symantec.com/support/ent-security.nsf/854fa02b4f5013678825731a007d06af/13669c4f8319b89e882574e5004e7328?OpenDocument
or
2) Restore the old SEPM servers certificate file.
http://seer.entsupport.symantec.com/docs/330611.htm
Lastly, I'm not sure what your final post was about, but I'm sure if you address the two issues above (in order) that you problems will go away.