After switching from 3.05 to 3.06, Real Time Protection and other problems went away. Then after 3 days the message came back on "Real Time Protection Layer Turned off", but in fact the protection was ENABLED. Clicking on fixing problem in Dashboard would not make it go away.
Then, unexpectedly, Web protection was Off, so I gave up.
About an hour later everything is ok, no Error messages, and when I checked Settings Protection all is ok.
I'm telling all of my clients to NOT ALLOW update from 2.xx to 3.xx until all the bugs are fixed, otherwise they and I will go nuts.
Weird stuff.