when creating some "custom user fields" with option to show them at the "Register Page" and selecting "Preferences", then the set "Display Order" is not respected. Meaning: the "Display Order" of these "Preferences Custom Fields" is not in the order which is set by Admin.
The "Preferences Custom Fields" seem to be always displayed at the bottom of the Fields-List at the Frontend of the Register-page. Not ordered based on the "Display Number" set by Admin.
Chris's response is correct. This is reflected in the ordering in the back end and there isn't anywhere that orders them solely be their display order to my knowledge. (That would then be a bug.)
The grouping of fields affects the display significantly on the front end. It controls where they show up to be edited and where they show up on the profile. This is one of the few places where they're "mixed" together so an order needs to be picked and is done so based on the group first.