5v and ground should be on the outside.
Sounds like you ran into the same harness wiring mixup that I had at first -- two similar colored wires that were reversed -- black and purple IIRC.
The harness is easy to reconfigure, so that's what I did with certain wires.
Scott
EDIT: Now that I look closer at this, I realize that the harness came wired as advertised -- it is a flaw in design and/or execution, depending on how you look at it.
Andy should probably consider:
1. Slapping his designers/beta testers for designing/not noticing the different arrangement of pins on UTrak + Spintrak.

50 lashes with a wet noodle!

2. Getting the right color wires (orange/brown) for x-axis on the next batch of UTraks. The UTraks shipped with the mini-USB encoder are already connected when they ship IIRC so it makes sense to align the UTrak wire colors to the Mini-Pac harness that customers will need to connect.