Here is my gnubg board theme that I had to swap the checker colors around after the recent update to show the analysis with the players swapped so the perspective would be the same as the GreedyGammon board. For some reason it was swapped when the jfmat file was generated and I finally got around to correcting it.
import gnubg board theme http://greedygammon.com/positions/swapCheckers.zip
Download the zip file from the link above and extract the file swapCheckers to your desktop
Open gnubg and go to Settings>>Board Appearance>>Import Design and select the file swapcheckers from your desktop