I believe it has to do with the position of the start button on its image strip. Since Vista's start button is not left-justified like XP's, then a skinned Vista start button will not quite behave like a skinned XP button. I have run into this as well.
The only solution I can think of is to include a separate substyle for vertical taskbars with a modified start button which is positioned in its image strip further to the left.
I don't know for a fact that this is the right answer, but this is my take on it.