I have the same issue, and the folders are not appearing in the same order as in the directory structure.
Quad Core 2.3GHz Intel, 64-Bit, Win 7
16GB Ram, 2GB Graphics Card
CV314-5: AutoCAD® Civil 3D® Design Straight Out of the Box: Going Where the Design Wizards Can't Always Go .....
I have always had to simply drag them into place. Even refreshing the Sheet Set Manager hasn't worked. It is best to drag the last file to the top, continuing until all files have bee reordered. This is also true for the Project Navigator's sheet tab.