Tried searching: Makerware and scaling efforts....

I use Inventor to create my objects, and save into the correct format, but when I open these objects in Makerware, I need to scale them.
I have gotten use to this, but I finally noticed the "runout" on round objects wasn't due to the accuracy of the Makerbot 2, but due to scaling issues.

On my current open object, I keep selecting for the X direction to be 59.51mm, and no matter if I select the 'uniform scaling box' or not, it is changing my Y and Z directions. If I hit Enter or click on a new line, the Y direction keeps changing to a new number, in this case, 59.65, and every new change keeps adding .01mm after hitting 'enter' on the keyboard.

No matter what I change, it will not let me make my objects perfectly round.

Has anyone else experienced this or: know why it happens or: what to do?

I am thinking this might be a file format problem, but I don't understand why it would happen. going from .ipt to .stl, then scaling in Makerware.

I still haven't found a solution to this.

I asked the same advice on the autodesk forum. If I hear any results, I will post back. Still open to suggestions for now. thank you.