When you implement FEP, you might need to troubleshoot certain things that require actually troubleshooting the Configuration Manager agent. The below steps should get you started - for complete detail on troubleshooting Configuration Manager, see http://technet.microsoft.com/en-us/library/bb632812.aspx.

Client side

Install the ConfigMgr Toolkit V2 it will make things a lot easier to investigate and will allow you to view the FEP policy internals within the ConfigMgr policy classes in WMI using PolicySpy: http://www.microsoft.com/downloads/en/details.aspx?FamilyID=5A47B972-95D2-46B1-AB14-5D0CBCE54EB8/

• Logs: - use the SMS Trace that comes with the toolkit  and check two locations for the log files: C:\Windows\System32\CCM\Logs and :C:\Windows\SysWOW64\CCM\Logs.

  • CAS.log – Package download issues - look for lines like Download location found 0 - \\SCCMSERVER.DOMAIN\SMSPKGC$\CMP00004\  or Download started for content CMP00003.1
  • Execmgr.log – look for something like: Successfully prepared command line "C:\Windows\system32\cscript.exe" "ApplyPolicy.vbs" or Raised Program Prelim Success Event for Ad:CMP20003, Package:CMP00005, Program: Install
  • DCMAgent – for any DCM issues
  • ClientLocation – SCCM connectivity issues – look for Current Management Point is SCCMSERVER.DOMAIN with version 6487 and capabilities: <Capabilities SchemaVersion="1.0"/>.
  • InventoryAgent.log - Hardware+Software inventory - Inventory: Cycle completed in 0.047 seconds
  • DataTransferService.log – This is probably where you’re going to find an error.
• PolicySpy (toolkit) - check the client info – see that you are connected to the correct server *just like info from the logs. Look for instances of CCM_ISV_SoftwarePolicy to find the FEP policies inside of the ConfigMgr policy classes.  They will be listed under ISV Data properties.
  • Use Ctrl+R (Request Machine Assignments) to try to speed up things
  • Use Ctrl+E  (Evaluate Machine Policy)
• Control Panel applet: Open Configuration Manager from the Control Panel
  • DCM: click the Configuration tab (you should have some baselines there), click Evaluate for the FEP Baseline named "FEP Monitoring - Definitions and Health Status".  Monitor DCMAgent.log, review Report (click View Report in the applet).  Note that the client only send state messages up every 15 minutes at a minimum, so it may take a while before definition status is updated.
  • Hardware Inventory: click the Actions tab, and then click Hardware inventory cycle. Click Initiate Action. Review the InventoryAgent.log file.
• Check firewall settings
• Ensure that at least the .NET Framework 2.0 is installed.  This is required for the DCM feature of ConfigMgr to function at all.
• Last but not least – try a restart

Server side

• Check in ConfigMgr to see how BITS is configured for clients: Site Management -> <Site Code> -> Site Settings -> Client Agents -> Computer Client Agent –> right-click and then click Properties. On the BITS tab, look at the throttling window and the transfer rates both inside and outside of the throttling window.
• Check logs in C:\Program Files (x86)\Microsoft Configuration Manager\Logs
  • CCM log – Server status, fallback status, ports etc…
  • Replmgr.log – replication issues
• In the Configuration Manager dashboard, check:
  • System Status
  • Advertisement status errors
  • Site Status errors
  • Check boundaries
• Check that you actually assigned the program: In the Configuration Manager tree, expand Software distribution, expand Advertisements, right-click the adverstisement, click Properties, and then click the Schedule tab.

And since there  are a lot of other things, you might want to check the Configuration Manager Support Team Blog https://blogs.technet.com/b/configurationmgr/