The GUI always tries to reopen last opened scripts and compile them on startup. If any such a file is however missing, the GUI doesn't report it any way and either skips it or just prints out an exception stack trace into the console. This behavior is often experienced when the tool is migrated to another folder and/or machine together with the user configuration file.
This should be improved. The GUI should at least show a message box warning user of the missing script. If a library included through Run or Include commands is missing, it is not necessary to print out the exception because the error is already reported by the editor.