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.
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.
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/