It is much better to flash with console completely off and external power applied.
Doing some small patching with console on then powering off with front button has caused random errors for me and made some functions not work until reflashed with a good dump cold.
The reason i suspect is that data is shifted around when console is booted, and powered off, so some conflicts happen when you power off after a warm flash. One such error i can mention is wifi not working after altering the mac address with the console on and then powering off normally, where as no errors occur when the same data is written with the console off.
If you must flash with the console powered on i suggest after the flash is complete that you power off the console with the switch in the rear of the console...this has proven for me to keep from getting any errors/glitches.