Yeah I know why. You will try to figure out every way that I could be wrong... but unfortunately for EVERYONE... I'm not. Your bios is not being deleted. Your pogo pins on your xapter are the problem. When you connect the programmer you give the little nudge needed to re-align the chip so that it makes contact on bootup. It doesn't really have anything at all to do with flashing. Next time instead of reflashing just give your box a light rap. ( I don't mean yell "Who? MIKE JONES!.. I mean hit your xbox)
I wish pogo pins weren't plagued by their constant misalignment but they are and so that's why if it's an option to have a pro do it at all most of us would recommend a soldered installation.