Sometimes, i've had a bug, but i'm not sure if it comes from your mod... since i've also installed a new mod which changes the IDX numbers in data/Terrain/Terrain.cfg. Maybe an interaction between the 2 mods ?
Well, sometimes, when starting a single mission, the weather is strange : clear sky (no clouds) + huge waves + heavy rain. Then, the surface water (waves) disappears, and all the units (and my U-Boot) fall immediately to the sea bottom.