Do fliers ignor other figs for movement purposes, the way we have always played is that they dont and that only HSS does that but last night my judge said that they do and only need to roll breakaway if they are based.
Whats the deal?

Your judge is correct. Roll breakaway, but otherwise ifnore characters for movement. A flier can move directly through an opposing character's square.

Your judge is right. The rule came around sometime between indy & universe.

Wow that changes somethings, thanks for the help!