Bingo! I was finally able to duplicate this, so looks like it wasn't a problem with your computers after all. The problem surfaces only with the original savegame, not with the two desync files you later sent. This is interesting. This suggests that if you wait until the desync, save, and then load that save and continue from it, you might not encounter the desync at all (I didn't). Now I've got an excellent starting point for finding this desync, though, since I can now both reproduce it, and I have a chaff-free version of your desync data. Thanks! I'll be back in touch shortly (hopefully), once I have this sorted.
EDIT: Turns out there is just as much chaff in these new ones as in the old. Evidently an extra call to random is occurring somewhere, and that's causing a lot of minor things to get slightly off. This could be due to other factors like an extra ship dying, or the position of a ship getting off quickly, etc. Now that I can thankfully duplicate the issue, I can see what's going on, though. Thanks for all your help with this, and your patience -- there is nothing more frustrating than a desync bug, I have to say.
EDIT2: I am able to watch the desync in action, so it's just a matter of time until I find it. Some of the ships are moving differently while in free-roaming defender mode. On one machine they finish off the sniper and then start heading east, while on the host they just sit near the wormhole and kill the sniper (these are both on the green home planet). The desync then happens when the next wave comes in and the ships are all in the wrong positions on the client. This save file that you provided me could not be more perfect for hunting this thing down, I must say. So don't worry about hunting up anything more for me now, I have absolutely everything I need.