I believe this is a question that will require hands-on assistance as you don't really have a general question that can be answered effectively here. One suggestion I can make is that during interrogation, you might need to add some controls to your hierarchy via the Windows Controls or Web Controls tab in your adapter. This is necessary for some controls that reside under others or are otherwise unable to be selected by the Interrogation Form. You might also validate that these controls exist within an application that your adapter is set to hook into. Process Explorer is a great tool for determining if an application is started by another. Perhaps this is actually a child process of your adpater's application and you simply need to set HookChildProcesses to True. 

If this is insufficient, you'll likely need to contact your account team to schedule some support from our professional services team members to take a look.