Baz,
Interesting that you raise this point. I also have some question about the focus results I get with Bahtinov mask. I had a hunch it works better on reflectors due to the absence of chromatic aberration, but I have not had a chance to prove it conclusively.
Craig did a good comparison of the mask to Nebulosity, but it was on a Newt. I'd like to see the same test on a refractor, just to check.
Let us know if you get to perform the test proposed by Terry - that would be the simplest explanation in your case.