After the .NET agent installation with Sharepoint site, it is generating many different type of errors including error 504. Site also stopped working completely.
Looks like the agent is getting initialized too early and thus causing issue with SharePoint.
Test with the following properties one by one and then both together.
Test 1)
introscope.nativeprofiler.generic.agent.trigger.enabled=false
Test 2)
The following will tune down the extra instrumentation.
introscope.agent.discovery.autostart.enable=false
Test 3)
introscope.nativeprofiler.generic.agent.trigger.enabled=false
introscope.agent.discovery.autostart.enable=false