Did a significant change happened when opening the game the two times? (for example, updating drivers, installing program, etc.)
Try deleting all of Pizza Timer's data from the directory %APPDATA%\Godot\app_userdata by deleting the Pizza Timer folder entirely, see if it fixes the issue. If not, please open a bug report on GitHub and upload the latest log (located on %APPDATA%\Godot\app_userdata\Pizza Timer\logs)