If you have available Server Visibility licenses (separate from machine agent licenses) then to enable server vis on those machine agents you'll need to go into the controller-info.xml file and flip the following attribute to "true" to enable that ma...
Looks like it's working correctly, what you're seeing are the calls it is making. What exactly are you wanting? Are you wanting to configure the identification rules? Those can be found on he left-hand side of your application under Configuration > ...
Are you sure you're starting the correct javaagent.jar? No logs generally means the agent didn't start. Did you follow all the steps in this document? https://docs.appdynamics.com/display/PRO45/Install+the+Standalone+Machine+Agent
You should be able to compare your scripts. In your Controller, when you go to User Experience > APPLICATIONNAME > Configuration > Configure JavaScript Agent, under 3. Save Config and Generate HTML Snippet, you should see a line similar to this:
<scr...
Essentially it's just a javascript injected in the header of your application, so the delay in IE might be in the way or order that it tried to run through the header. It'll be an interesting experiment to try and run F12/inspect element on an IE and...