Know this thread is primarily dealing with the Linux version but I am seeing similar issues on Windows (Vista with an ATI Radeon gpu) with the space center and in the VAB and SPH where textures don't load correctly. on the space center screen sometimes my whole facility will be under water. This shows up both with modded and stock instances of the game for me and also pops up if my windowed instance of the game looses focus, about the only fix I have found that works is to open the settings menu and hit either apply or accept which usually forces the game to reload the textures.