Thanks for all of the detailed information you posted. It appears that you have already tried reformatting the controller in 'Safe Mode'. Could you capture some data from a Console Out serial connection and post them to this forum as well. Perhaps it will offer some more information as to the state of the controller. If we are unable to obtain useful information from the capture, you may need to ship the device to us under an RMA. See page 9 of the 9012 user manual linked below for information regarding the Console Out functionality.
OPERATING INSTRUCTIONS AND SPECIFICATIONS CompactRIO NI cRIO-9012/9014