Don’t know about the console switching logging off, but here’s my 10 cents
The logging on/off flag is persistent, so once you set it on in the E1 it should remain that way. I 'm not sure what a firmware update does with it though.
To enable it, I use Midi-Ox and send the appropiate SysEx from there into port 3. The sysex string is in the SysEx part of the documentation, just don’t forget to set the flag in the desired state.