There are some cases where a custom application will undergo an application shift into another application.
To prevent an application shift on the custom application, set the proper parent app in the custom application options. The parent app will vary depending on the custom application.
From the WebGUI, go to Objects > Application > Select the custom application and in the Properties section set Parent App to the appropriate application.
For example: Setting the parent app to web-browsing using a signature to match specific HTTP headers.