Noticed this while looking into a related issue.
The following steps re-order the UV layers.
- With the default Cube, add 2 UV layers.
- Enter edit-mode
- Add a Torus
- Enable "Generate UVs"
Notice that before adding the torus the UV layers are UVMap, UVMap.001.
After adding the UVMap.001 becomes the first UV layer.
This looks to be caused by object join code.