While these anomalies are almost always somewhere in the game for me, with my GeForce 440MX I find that it works best with older drivers. With the latest drivers the invisible ships and even problems in other games are almost always there, but if I use driver version around 44.03 it works best for me. I would suggest properly downgrading your driver(i.e., use Detonator Destroyer to properly remove).
http://forums.guru3d.com/showthread....threadid=67799
That site has a good howto guide to properly remove the drivers. Sorry if you already knew that, but it is *extremely important to properly remove the drivers, especially when downgrading.