One thing that may help in advanced mode is putting all your compiled code in any anonymous function wrapper:
Change the last line to:
if it needs to execute the code block as soon as it's loaded.
This stops conflicts with any other scripts apparently in the global scope which can cause issues. For example if the Jquery.min is in the global namespace there will be conflicts between minified variable names as the closure compiler declares things such as:
var s = true, x = null, v = false;
These might conflict with Jquery minified code.
You probably know all this but just incase it's the issue.