In winding my warp for the turned twill (S5 E 1) I warped some of the stripes holding two threads and some single. It just so happened that it corresponded with A and B blocks. What I'm experiencing is that when weaving, the threads in the A blocks (threads held double in warp) rise higher in the shed than the B blocks (threads held single in warp). Is this normal? Should you not mix multi-single threads in a warp? I'm weaving on a Jane.

It shouldn’t matter. Have you woven a small sample to see how it weaves up? Could your tension be different depending on how many threads you had in your hand?