RunSpeed and MoveSpeed are two different things. So RunSpeed is supposed to be 4.0, like previously mentioned by someone else I think.
Base speed is supposed to be .77 so if it's saying .85 there's something wrong. Are you sure you're loading only the fallout .esm at the top of the list and not that+some other mods .esm?
I'm not sure exactly why the console commands work - eg, where the changes are 'written to'. If they are written into the save files themselves, then yes they're going to persist within those save files whenever you load them up. Only saves from before or after you altered via the console will be 'normal'.
With mods, if you deactivate the mod, most of the time it should go back to the original state even when you reload a save because you no longer have an override file working on the game. Not always (items for example, sometimes persist), but for something as simple as run speed, it should. Does for me.
Hmmm the variable is set to 90
It's .77 in my GECK, with only the falloutNV.esm loaded.