Sounds like you have a body inside a subcomponent and the subcomponent has been rotated. That is the only way I can reproduce this.
When I did that, I noticed that the subcomponent origin axis are turned because the compoenent is rotated. The move body dialog matches the rotated subcomponent origin, not the universal origin. Is this the situation you are in? If so, it's as designed.
*EDIT* I just saw a demo of what you describe in the production version you are using, the image below is made in our development build. It's possible this has been fixed and would be released in the next update.
**EDIT** Working with DEV I understand now what is going on.
Move orientation works in two ways.
Method 1: Right click on a body or component in the browser, you get the behavior seen in the image above. The Move triad is perfectly aligned with the origin of the owning component, be it the top level or a subcomponent.
Method 2: Start Move and pick the body. You'll see that the manipulator can point in any number of directions and snaps to all sorts of interesting points. However, in this case the "vertical" vector arrow, the one facing away normal to the object face, will always be Y according to the dialog box.
Phil Eichmiller
Software Engineer
Quality Assurance
Autodesk, Inc.