Yes this happened to me. The first was right after I had added the Pulse Script, but before changing the User Settings on Chrome. It tried to update automatically, but I managed to catch it the first time.
Unfortunately, I was not so lucky the second time

I had been in rootland for about two full days, and suddenly I turned it on and it said "Your Google TV Has Been Updated"...
I don't know if they added an automatic patch, or if it just cued itself up on boot and I am pretty darn sure I followed the instructions to the wire... But my hopes and dreams of a rooted GTV has been short lived I'm afraid...