Wow. Is this the replacement board for your FF board you reported as burnt in January? If this has happened twice in the same place -- HBP power -- then maybe the HBP is defective. For example, if the resistance is too low on its traces, it will draw more power than it should. Also, when the motherboard board was replaced, the wiring harness should have been replaced also: the end on that scorched connector may itself be damaged and have insufficient contact area. That causes increased resistance and thus abnormal heating at that reduced contact point.
And there is a rare event which happens on AVR processors: something goes wrong with the .hex file download and the bootloader itself gets nuked. Since that first runs when you start the bot, even when you're not downloading firmware, this then makes the uprocessor not work correctly. It starts the bootloader which, when no download happens within a few seconds, is supposed to then start the bot firmware. But if the bootloader is nuked, the bot firmware never starts. This unfortunate event has nothing to do with the particular firmware. It is just some sort of comms error which glitches the desktop / avrdude / uprocessor comms. We've see this come up now and then on the makerbot-operators forum even with just MBI firmware. And it comes up over in Arduino forums as well. If this has happened, it takes an AVR ISP programmer to put a new bootloader onto the processor. It's not rocket science, but isn't something most people are equipped to do.