Ok, so I played an 8 hour game (thats right, 8 hours) - I'm actually on vacation all this week - using the sync.exe file and we NEVER got a desync.
We were playing on my LAN so that may have been the issue, we also saved the game 3/4 of the way through and transferred it to another computer and ran it again (still using the sync.exe file) and still no desync.
I'm wondering if the desync occurs on latent connections because it happened every time we played over direct IP access. I have a fast FIOS connection and my buddy has DSL.
I'm wondering if that has a lot to do with it.
We were also initially playing on a really slow laptop and my really fast desktop, just to see if that had any affect on the problem, and it appears that the only difference was the fact that we were playing on a LAN.