Try to map as clean as possible is the only thing I can say. I've had this stuff a lot as well. Make sure that every edge of a brush you create is on the grid. You can do this easily by selecting brushes and pressing CONTROL+G. This often messes up your map though, best thing is to make sure everything is on the grid while working on your map. Oh and yeah, this was about the invisible walls.
I have never had problems with textures floating around where they shouldn't be.
Texture loss can be caused if you have a caulked face(of a brush) touching a face with a texture. Just make sure there is a small gap between the caulked face and the textured face.
