This might be helpful.....
In the following video you'll find instructions for doing Fair Isle (two colors) but without the floats - the yarn is handled in such a way that it is woven into the back of the fabric.
From your query, it seems to me that the techniques shown in this video, particularly stitches #3 & #4, might solve the "twisting" problem you're having. Without practice this might seem complex but I found it very learnable with some practice.
Please let us know if you find this has use in your project. Apparently it's a big issue for other knitters and hopefully this will solve that dilemma!