That's right, auto focus doesn't work at high ND settings. So I learned to operate the Vari-ND duo this way:
- first set the ND effect to minimum
- adjust the polarizer ring as desired
- focus the image, then switch the lens to manual focus to essentially lock it in position
- adjust the ND ring to desired level, and take the photo


Obviously, this isn't so convenient when taking a portrait picture! So far I have only used it for landscape work.