Have you restarted the Agent Coordinator service and then standalone application service in a sequence after configuring the standalone app in configuration filel?
Do you see the coordinator service process and application service process entry in the agent log file ?
Please provide read and write permissions to account under which the executable is running at DotNetAgent folder ( Logs directory ) and <AppDynamics_Agent_InstallationDirectory>\AppDynamics folder and then restart both Agent Coordinator and the application service. After that apply the load on the application and then check teh behaviour.
Let us know if it helps or you have any question.
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