Hey, I had the same problem for one project by being a bad boy....
I simply wanted to make a backup of my project, so I copied the project folder over to a new folder... and updated the names files accordingly.
I could compile and run, but it ALWAYS asked me "Do you want to build it now?" message.
This doesn't happen if I create a new project... and then drag the media over, and then copy/paste the code into the new main.agc file.
I guess there is more going on here than meets the eye.