Mrwebb,
Basically, this warning is telling you that you can't edit a template because the template is currently in use. This is not a bug -- it is intended behavoir to safegaurd against people changing the template and thus corrupting existing applications.
Sorry, with this release, you can not edit or change a template when it is being used.
in order to change your template without recieving the warning/alert messages, enter the forum which the applicant forms are installed to. You should find 2 applications in your forum. Find a submitted application, choose the edit application icon, check the 'delete application' checkbox and click submit.
Delete both applications that are currently in use, and you should then be given the ability to change the template around without recieving the Alert messages.