I ran into something like this as well. I had wind walk, phase shift, and permanent invisibility on the same character. There were many strange issues. I eventually just removed the permanent invisibility (and later phase shift because it didn't do what I wanted it to).
Seems like you can't do that, though. You could try triggering the phase shift ability using a dummy spell. It is worth noting that phase shift doesn't protect the unit from everything - particularly triggered damage - unless you are already checking for phase shift buff in all of those. It is probably just better to trigger the effect and make the unit invulnerable.
Alternatively, you could look for another way to disable auto attacks. I don't know of any, though.