Hey Wes,
I just tried to do this with the new version of SP (0.5.0) and still have the same problem...
The attached image shows a random layer order, if I try and re-arrange any of the layers up or down in the list (drag and drop), the mouse pointer changes to the little circle with a dash (the "cannot do this" icon, for lack of a better name

) when you click and hold and try to drag the layer, and nothing happens when you release.
This is not a huge issue, I know it is best to define layers first, but can come in handy if I wanted to add a new map underneath the paint layers later on for instance.
Thanks again, and btw I really like the additions to 0.5.0!