Finally pinned down the problem and its between this mod, prepare carefully and humanoid alien framework. In fact running the following order and nothing else still poses a problem:
core/edb/alien framework/facial stuff/alien faces patch

I can delete facial stuff and the problem goes away. Same by deleting the alien framework. Its strange though, I can run a game with edb and facial stuff, or edb and humanoid alien framework,but not all 3 together.