This particular discrepancy has to do with whether the player on roll is on the near side of the board. Notice that you can get from one XGID to the other by reversing the string and exchanging uppercase and lowercase letters.
In my "Export Position to Clipboard" menu, I usually have "Player on roll always at the bottom" checked. I'm not sure if this checkbox is the culprit, but in any case, the first time I tried Nack's position, XG automatically flipped the position at some point.
In any case, I have tried various things to see if I can get inconsistent XGR++ evaluations when the position is flipped, but so far without success.
By the way, I know that XG has some subtle bugs associated with flipping the board in this way, but it doesn't seem that that can be the whole explanation.
         
 
         
 | | White is Player 2
score: 0
pip: 194 | Unlimited Game
Jacoby Beaver | pip: 197
score: 0
Blue is Player 1 |
|
| XGID=-bb---D-C---dD---c-d---AAB:0:0:1:21:0:0:3:0:10 |
| Blue to play 21 |
| 1. | XG Roller++ | Bar/24 Bar/23 | eq: -0.0824 |
| Player:
Opponent: | 48.04% (G:12.42% B:0.58%)
51.96% (G:14.42% B:0.78%) | |
|
eXtreme Gammon Version: 2.19.211.pre-release
  
  
| | White is Player 2
score: 0
pip: 197 | Unlimited Game
Jacoby Beaver | pip: 194
score: 0
Blue is Player 1 |
|
| XGID=baa---D-C---dD---c-d---BB-:0:0:-1:21:0:0:3:0:10 |
| White to play 21 |
| 1. | XG Roller++ | Bar/24 Bar/23 | eq: -0.0824 |
| Player:
Opponent: | 48.04% (G:12.42% B:0.58%)
51.96% (G:14.42% B:0.78%) | |
|
eXtreme Gammon Version: 2.19.211.pre-release