When you're actually looking at a form then yes you will see Form Builder in the breadcrumb trail. Unfortunately I'm not sure there's much I can do about this. The best solution is probably that you set your custom thank you page to have a link on it back to the list of application forms.
Or, perhaps you could publish your thank you page at /application-forms/thankyou, or similar, so that once users reach this page the breadcrumb trail will lead them back to the main Application Forms page.
(i.e., create the thank you page under Application Forms but don't put it in the navigation menu. Then set this as your custom thank you page for your forms, so that users are sent there after form completion)
Hopefully this makes sense :-)
Joe - Voice Admin