And to continue the metaphor: As long as you have multiple legs running in unison, things will work great, and you'll get a lot more power than you would from just one leg. But if one of your multiple legs lags a long ways behind another, everything gets tripped up horribly.
That's what was happening, at least for me. E.g., I would click on a unit, which one thread apparently took note of. A different thread was apparently supposed to get the message that that unit had been clicked on, and make a noise and switch the highlight circle to this unit to show that it had been clicked on. But, for some reason, this second thread was lagging way behind, so this notification wouldn't happen unless you wait a really long time (like 10 secs). Interestingly though, you could hit M to initiate a move sooner, and it *would* display movement paths from the new unit you had clicked on, rather than from the old unit that still had the highlight circle around it. So apparently the movement paths are displayed via a separate thread from the one that updates the highlight circles in the UI -- perhaps the same thread that took note of my initial click, or perhaps a third thread.
Anyway, I think their theory was to separate a lot of the AI and core mechanics of the game into one thread, separate from another thread that took care of displaying things on the screen. In theory, this allows the user more flexibility to navigate the map between turns using the second graphical thread, even while the first AI thread churns ahead full speed. But, in practice, there are apparently some glitches in the graphical thread that end up making it fall far behind the thread(s) that process more of the functional mechanics of the game, which ended up making the user interface unbearably sluggish, at least for some of us.
As far as I can tell (having tried only a few turns with the multi-threading disabled) you don't lose much in the way of functionality by disabling it, and the speed and smoothness increases are well worth it.