Save Changes?
 

I have a nightly build and over the weekend my build only ran on Saturday night, not Sunday night.

When I check the build PC, my build is open and asking "Do you want to save changes? YES, NO"
It looks like this is from Saturday night and this caused Sundays build not to start because the Saturday build was still running.

I am at a loss on why this is happening or how to stop it -- any suggestions would be greatly appreciated.

Sounds like something in your build modifies the project (the GUI app will prompt for unsaved changes to the project on exit). If the build is changing project macros, one alternative would be to use global macros instead (which are saved automatically on exit). Otherwise, save the project file at the end of the build:
http://www.kinook.com/Forum/showthread.php?threadid=245

You are correct about changing Macros
I added the step and it works fine.

Thank you!