If you start a new game using a simple map script, then all features are primary features which from the point of view of the game engine are the same as the features without the multi feature mod.
In other words: The probability that it is just coincidence is very high.
Far more likely is that we have a memory corruption issue. Anyone tried unpacking the terrain textures from the FPK?
I'm not sure if it makes a difference, but using the terrain.fpk from SVN3564 with more recent versions still causes black tiles for me (or crashes the game, I'm not sure which as I've tried replacing each one at a time and don't remember which did what---as I said, I've tried some crazy things to get it to work).