Hello,
What comes to my mind is watchdog SWT.
Debuggers by default disable watchdog in debug mode, so you can perform debug.
Make sure your SWT is disabled / services correctly.
You can check RGM module DES and FES modules for any latched reset sources.
However, when I reset or restart the board without the debugger, the application does not run.
Also I am not sure what "does not run" means....
Is SW stuck in some loop,. reset, exception, etc..... ?
Additionally debuggers perform various initializations like RAM initialization to be able load binaries for communication with device via scripts, which are not always visible to user.
You can also check FCCU NCFSx registers to see if any fault is latched there, this will give you a good hint where to look.
Best regards,
Peter