Well it’s been a couple of times when I updated with the routeros-x86 package and I can’t trust this update at all. I’ve gone back to the reliable all packages update because it seems to ignore the wireless that is installed many times and fails to update it at all. Very bad when it requires our tower climber to climb the tower to change out with a different AP setup because of this issue.
have you upgraded from 2.8 or from 2.9rc ?
router-x86 you should use, when upgrading from 2.9rc 
Twice from upgrade 2.9rcx to 2.9 final.. Most of the times it works but it failed twice. So can’t risk it with the boards on the towers already.
Updating the late 2.9RC’s and to 2.9 stable, I had an AP lock up a couple of occasions when doing a remote ftp upgrade/reboot, i.e. it didn’t come back up and needed the power cycled.
Hardware = 266MHz x86 non-MT Routerboard-like platform. Normally incredibly stable and can be trusted.
It was 60 miles away but didn’t have anyone “on” it at the time.
Not sure why it happened, but it did …
Regards