I've pin-pointed an issue with the Project Wizard, projects that contain a significant amount of folders will cause the Advanced Installer process to become unresponsive when clicking Launch application after install, then finally show the file dialog hours later. I made sure it's an issue by testing the wizard using a similar-sized application which has few folders but a similar size to the application I'm currently having issues with, and noticed the issue didn't exist for this situaiton.
On another note, Advanced Installer will also hang for a minute when building the application and canceling during preparation. This is with a project that contains a lot of folders.
In what regards your issue, I am not sure why that happens. Could you please send us a a buildable sample (the project does not need to contain any files as long as it replicates the behavior. For example, you can strip down your main project and send it over if the behavior still reproduces) by e-mail at support at advancedinstaller dot com so I can investigate it?
Also, is this behavior reproducible on multiple machines? Or is it happening only on the developer machine?