I have been seeing an issue throughout multiple designs in which the AT91SAM9 resets properly during a power cycle.
It's when I issue a user reset to the NRST input that sometimes I get a ROMBOOT issued on the serial debug port and the
Bootstrap never tries to find code. It's a real problem when you are trying to field upgrade code. The only way to get out of the situation is to power cycle.
If anyone has seen this issue, please let me know the steps for resolving the problem.