Ace2 mods use dewdrop-2.0, which attaches icons to the border of the map. Since squeenix changes the map to be a square, ace2 icons go along the sides of it like that.
Unfortunately, most other mods simply think of the minimap as a circle, and simply change the icons radius from the center of the map. So, non ace2 mods will be positioned inside the square, and look a little odd.
You'll have to donload something like DetachedMinimapIcons from wowinterface.com which will let you move non-ace2 icons anywhere you want.