After you open Tools > Board > Boards Manager and wait for the downloads to finish, do you see any error messages in the black console window at the bottom of the Arduino IDE window?
I get this one: http://downloads.arduino.cc/packages/package_index.json file signature verification failed. File ignored.
Once I can see what you have set for "Additional Boards Manager URLs", I'll be able to understand the cause of the "no protocol:" and provide instructions for you to fix it.
For the MKR issue, it went back to normal for a little bit and then when I plugged in my MKR, all the options disappeared from the boards manager again. I then tried your suggestion and nothing changed.