The flash.py script takes care of putting the board in recovery mode and flashes the board and puts back the board in normal mode. If you plan to use bootburn script instead of flash.py, then we have to take care putting the board in recovery mode/normal mode.
When you access the tegra via minicom make sure you put the board in normal mode.
Did you test flashing with flash.py when board is in normal mode? Please share the logs. This should confirm if it is hardware issue.