The PC I'm on right now was upgraded from Windows 8 (which ran flawlessly) to Windows 8.1 yesterday.
After untold number of problems - some of which seem to be tied to a motherboard that was certified for Windows 8 -- but magically NOT for 8.1 according to MS - I've gone back to Windows 8.
I've NEVER experienced an issue with an "uncertified motherboard" during a dot-rev upgrade with ANY OS. This is a first for me, and MS has some 'splaining to do based on the forums I've been reading between yesterday and today.
Hope you get the upgrade straightened out soon. I know Toshiba had me download lots of little hardware updates preparing for 8.1 before the release. That may be your "motherboard" problem since so much is on the motherboard these days.