See SCN 4164.

The universal programmer uses the JTAG port to program the boot on 5386 boards and to perform other tests.

The software in the universal programmer was not erasing both boot segments in flash for any 5386 board rev greater than D. D and higher use the same flash erase algorithm. Prior to erasing flash, FlashWizard was modified to lie to the programmer, telling it that these boards are Rev D boards.