If you complete those steps and still do not see business transactions in the Controller, check if your managed code runs in the DefaultDomain. If so, you must configure the agent to instrument the DefaultDomain.
Check if Your Application Runs in the DefaultDomain
If you are unfamiliar with your application's managed code, you can use the agent logs to identify the AppDomain.
Open the agent log: Windows Server 2008 and later:%ProgramData%\AppDynamics\DotNetAgent\Logs\AgentLog.txt
Search the agent log for AppDomain.
Few log entries contain AppDomain when the agent starts up. Look for an entry by dllhost or your instrumented application similar to the following:
2013-12-16 08:23:02.3120 3068 MYPROGRAM 1 1 Info Configuration appDomainName=DefaultDomain appDomainId=1 iis-app=null site=null port=null appPoolId=
2013-12-16 08:23:02.6240 3192 dllhost 1 17 Info ConfigurationManager Not instrumenting DefaultDomain for pid 3068
CODE
In this example, MYPROGRAM is the name of the instrumented standalone application. You can see the name of the AppDomain in the log entry, appDomainName=DefaultDomain.
Instrument the DefaultDomain
Open the config.xml file for editing as administrator. See 'Where to Configure Agent Properties' on Administer the .NET Agent