Hi
I had a similar problem. The themes with the new kernal would work but when I loaded my own skins up came the original R4DS skin.
The directories where correct.
I decided to delete the _DS_MENU.SYS from the root directory and then rebooted the R4. All Work
So maybe when updating your themes, delete the _DS_MENU.SYS and let the R4 recreate it when it boots up next time you turn your DS one.
Hope this helps