I see the same type of problem with my SuperMicro X7DCA-L with the latest BIOS (R1.2a), though I don't even have to change anything for it to happen. The machine just randomly decides to move things out of the excluded list and/or change the boot order. Sometimes I can reboot several times in a row before it happens, but it happens regularly.
I'm assuming that just like they can't be bothered to properly document their BIOS settings, keep their manuals up to date or package their BIOS updates packages with all of the parts needed to actually install it; they can't be bothered to write a properly working BIOS. This is especially sad given the premium they charge for their products and the market they're supplying.