Shintai summed up the situation perfectly. The lag doesn't seem related to any particular time of day, but it does seem related to the massive Germany-France-Poland war going on, unfortunately this war never ends so I can't really confirm it. As he says, it wasn't present in even the slightest way prior to update 2, and if anything the European wars were even bigger then.
I've tried both 16 bit and low unit resolution, as well as everything else in the thread, so I can't see that'd be the problem, and considering the small memory footprint I mentioned earlier, I can only think it's thrashing the CPU in some way. My hugely unprofessional guess based on what I've seen is that it may be something to do with the AI putting units in or out of reserve en masse. This, however, could be a complete red herring.
Running a P4 3Ghz and a 9800 Pro, for daikyu's benefit.
I'll PM you my dxdiag rather than spam the boards.
Edit: I'll also try one of the other continental maps to see if I get similar issues.