Just a heads-up that the internal materials don't convert automatically either! Actually I have some other support questions, is it OK to post here or would you prefer an e-mail?
Yeah, I already did some tests and noticed the same problem with the internal materials. I will try to improve the situation and remove the shader for the 3D cursor too, but I will probably need a few days, sorry. (Too many other projects...)
Just write your questions where you feel the most comfortable!