There are a few known issues regarding the Cairngorm plug-in.
First, it may not be able to find existing controllers. When you create a controller using the plug-in, it gives it a unique ID using a private static constant UUID. The unique ID is used internally by the plug-in to associate the controller with its configuration. If a controller doesn't have the UUID constant, the plug-in will ignore it. If you have an existing controller you will need to add the variable manually, but make sure the value is unique.
Second, when you add a new command it is automatically added to the controller, and to enable this the plug-in uses the Flex Builder Code Model API to rewrite the controller with the new command added. There are some limitations to this system, as the plug-in will ignore the following:
The use of the implements keyword
Function code blocks (if you need a custom function, put it in a base class)