Turns out I was wrong about the slight change, not sure what was causing it to turn off after 20 seconds but when I tried to turn it on today it did the usual "keyboard lights up, cooler boost button works, keyboard backlight control works, no MSI logo and after 30-60 seconds the CPU fan kicks on"(basically everything that. So I wiped and flashed the stock bios chip to the newest bios version fresh from the MSI site (119), removed the ebay chip (116) and reinstalled the freshly flashed stock chip. Absolutely no change.

For giggles I tried turning on the board without any bios chip installed to see if there would be a different reaction and there was not. I suppose this would make sense as a bad flash is no different than having no chip installed.

After spending several hours pouring over the MS-16J2 /1792 schematic, I'm at a complete loss to why this isn't working. There are no missing (that aren't supposed to be) resistors around the bios chip, I double and triple checked that all the solder points on the chip were solid, and even went through the EC reset procedures more times than I can count. Heck I even ended up digging through every thread in the MSI section of http://vlab.su/viewforum.php?f=60 and despite the russians doing some seriously advanced motherboard repairs I found nothing of any real use other than links to schematics.

Could this somehow be the EC firmware being bad? It was perfectly fine before I bricked the bios and it appears to be in working order (power button works, keyboard lights up, FN commands work, etc) so I'm hesitant to yank it off.