Hello Jack,
The issue is solved. Seems there was a permission problem in the AFM_HOME to generate the properties file.
Initial Setup (where issue was there)
1. I used portable tomcat just extract the zip file and use the tomcat by just adding jdk path in catalina.
2. open the command prompt as administrator and run the tomcat startup.bat to access the services.
3. Not sure even though i was running tomcat in administrative privilege AFM profiles was generating any properties files.
Second setup ( where issue solved):
1. I downloaded tomcat installer tomcat7.exe
2. Installed software as service with administrator privileges
3. Re-Deployed all the war files
4. added the JDNI connections required for state manager
5. created the AFM profiles with out any issues, tomcat was able to generate the properties files in AFM_HOME/conf/afm
6. JDK is 1.7.0.79 32-bit and tomcat is 7.0.72 32-bit, CA advance authentication 8.1 32-bit
Thanks,
Ravi