Same thing has happened to my resellers and my personal self. Emsisoft will ask you to reboot once and it reverts to version 8 with File Guard disabled, then asks to reboot again and goes back to version 9 with File Guard disabled. I then proceeded to reboot a 3rd time, turned off all guards and turned them back on again and now all is back to normal.
I have advised Arthur about it, he has let the team know. Can be something related to Beta 10.
Let me know if you have any questions.