guess you messed with some tools. Did you try some activating stuff (KMS) prior to check update with store? Do you have all updates installed for w8 which are essential to get the store 8 > 8.1 update showed? Perhaps an outdated bios bug is around to cause some problems. Lot of stuff to be done to get the box running ....
I have tried: Windows 8.0 media center x86 (my personal free wmc key) activated over phone --> and tried via store update to win8.1 (crash at restarting ...after it was updated to win8.1)... Windows 8.0 enterprise x86 (activated with KMS tool) --> and tried via store update to win8.1 (crash at restarting ...after it was updated to win8.1)... but if will Windows 8.0 works another 5 year it will be ok ...