Some clarification is needed: do you mean that the pins appear to be in the wrong order? Or am I barking up the wrong tree?
If the pins are in a different layout, they can be changed with care, dexterity and good planning! There are few layouts, two of the most common being the Intel reference and Gigabyte-derived layouts.
I can provide more info (or you can Google for USB header layouts) if this I'm on the right lines.