Found another bug...
It seems that my soldiers are stuck to ground level. I cannot go up any stairs.
This has happened to me on a level called "The Gate", the African suburb, the Hills and crashed harvester maps (all the maps I've played since I noticed this).
It affects level changes in ships (ie stairs in the Harvester) and also changes in landscape (ie cannot even get to the harvester in the Hills map).
It affected my game compiled on 1/1/11, and also a game that I compiled 30 mins ago using Mutons script with the "clean" and "download" map options ticked.
As always, my system is Windows 7, AMD Phenom II X3 720, 4GB RAM, ATI 4850 GFX.