SlowCheetah configuration settings in app.config.deploy and not .exe.config

Question

I am using the latest version of SlowCheetah in an existing WPF project that I have that has already used ClickOnce.

I am trying to provide various application parameters (applicationSettings node in app.config, those that form the Settings.settings file) for each environment. When I publish, I get app.config.deploy (with correctly converted settings inside), as well as the ProjectName.exe.config file, which did not change the settings.

When someone installs the application and launches it, it simply uses the settings inside ProjectName.exe.config (which is true), and obviously the converted settings in app.config are ignored. Is there another step to get SlowCheetah to transfer the converted settings to exe.config instead?