AppGameKit doesn't support Source Control., so yeah... when you build it is going to save the source then compile it.
You'll see this behaviour in ALL Editors without Source Control Enabled.
While I'd love to see it added to AppGameKit (especially for Team Projects, where you want multiple people working from a common codebase)... I'm not going to hold my breath on that.
Mind beyond that, keep in mind that there is no AutoSave that occurs... so if you don't compile in a while then it isn't going to Autosave the Source.
The Undo Queue isn't affected though.