No, completely changed. You used to be able to ignore as many as you needed to, and then when you want to make further changes you could simply say change all. Quark knew you ignored the "first batch" for a reason and "change-all" ONLY changed any subsequent ones you want to change.
For instance if you have an area where the first part of text is a listing with words and numbers, and you knew some should not change, you could "ignore" those, and when you then got to the purely text area tell it to change "the rest" by saying change all.
If in fact this was purposely chaged functionality within quark, then quark should have made it known in no uncertain terms. I believe it to be a bug that nobody caught. If I truely wanted to change all, I would have said that immediately in the find-change box. Then I would expect a change all to affect all. But when several are skipped, why then go back and change "more"??