[quote user="David Luca"] then make a change to the program, recompile and wait the program to reload[/quote]
how are you doing the above steps? each step manually or using the "Debug" button?
[quote user="David Luca"]So then I exit debug mode and press Debug again but GEL is not executed.[/quote]
The C6748.gel file does target initialization on target connect. If you exited debug mode and the pressed the "Debug" button, it should try to start the debug session and re-connect to the target. If the GEL is not executed, there was some issue with the target connect (unless you modified the GEL file to change the default behavior)
[quote user="David Luca"]Then a third time retry I can go back into Debug mode and start my program. [/quote]
Was the GEL file initialization successful this time?