If I understand this correctly, you're saying that when arbitrarily rotating a brush, the textures shift? As far as I know, this is either normal, or a bug in Radiant.
In my opinion, the best answer would be to never use arbitrary rotation. Use edge or vertex manipulations instead. They come with their own problems, but arbitrary rotate will misalign vertexes like crazy, which is even worse. However, the texture coordinates will remain the same if you're doing a vertex or edge edit.