Thanks to Ken and David for double checking the fixing tool.
I dont know what happend in your initial RO.
Also the fixed position look strange to me. the error are
0.0085 for 13/9 6/5 0.0023 for 24/23 13/9 (note: the error is the same no matter how many games are rolled) Your posted fixed position show errors of 0.008 (looks right) and 0.000.
Rounding cannot explain how it went from 0.0023 to 0.000. The process of the fixing tool is pretty straight forward: calculate the delta and add it to the equity (and also fix the winning chances and the internal RO data). could you send me the files ?
Here are the RO I get(made in V1 , but posted with V2 so it displays 4 decimals)
With Opening book. 
              
 
              
 | | White is Player 2
score: 0 pip: 167 | Unlimited Game Jacoby Beaver | pip: 167 score: 0
Blue is Player 1 | |
| XGID=-b----E-C---eE---c-e----B-:0:0:1:41:0:0:3:0:10 |
| Blue to play 41 |
| 1. | Rollout1 | 13/9 6/5 | eq: +0.0031 |
| Player: Opponent: | 49.83% (G:14.10% B:0.56%) 50.17% (G:14.29% B:0.89%) | Conf.: ±0.0244 (-0.0213...+0.0275) - [60.1%] Duration: 11 minutes 05 seconds |
|
| 2. | Rollout1 | 24/23 13/9 | eq: -0.0013 (-0.0044) |
| Player: Opponent: | 49.75% (G:14.46% B:0.63%) 50.25% (G:13.48% B:0.63%) | Conf.: ±0.0233 (-0.0246...+0.0220) - [39.9%] Duration: 9 minutes 18 seconds |
|
| |
1 1296 Games rolled with Variance Reduction. Dice Seed: 7636419 Moves and cube decisions: 3-ply
|
eXtreme Gammon Version: 2.00.160.beta
Without the Opening book.

              
 
              
 | | White is Player 2
score: 0 pip: 167 | Unlimited Game Jacoby Beaver | pip: 167 score: 0
Blue is Player 1 | |
| XGID=-b----E-C---eE---c-e----B-:0:0:1:41:0:0:3:0:10 |
| Blue to play 41 |
| 1. | Rollout1 | 24/23 13/9 | eq: -0.0035 |
| Player: Opponent: | 49.68% (G:14.48% B:0.66%) 50.32% (G:13.63% B:0.64%) | Conf.: ±0.0233 (-0.0268...+0.0198) - [54.0%] Duration: 9 minutes 15 seconds |
|
| 2. | Rollout1 | 13/9 6/5 | eq: -0.0052 (-0.0017) |
| Player: Opponent: | 49.54% (G:13.99% B:0.58%) 50.46% (G:14.27% B:0.90%) | Conf.: ±0.0244 (-0.0296...+0.0192) - [46.0%] Duration: 11 minutes 02 seconds |
|
| |
1 1296 Games rolled with Variance Reduction. Dice Seed: 7636419 Moves and cube decisions: 3-ply
|
eXtreme Gammon Version: 2.00.160.beta
fixing the initial RO with OB

              
 
              
 | | White is Player 2
score: 0 pip: 167 | Unlimited Game Jacoby Beaver | pip: 167 score: 0
Blue is Player 1 | |
| XGID=-b----E-C---eE---c-e----B-:0:0:1:41:0:0:3:0:10 |
| Blue to play 41 |
| 1. | Rollout1 | 24/23 13/9 | eq: -0.0035 |
| Player: Opponent: | 49.68% (G:14.48% B:0.66%) 50.32% (G:13.63% B:0.64%) | Conf.: ±0.0233 (-0.0268...+0.0198) - [54.2%] Duration: 9 minutes 18 seconds |
|
| 2. | Rollout1 | 13/9 6/5 | eq: -0.0053 (-0.0018) |
| Player: Opponent: | 49.54% (G:13.99% B:0.58%) 50.46% (G:14.27% B:0.90%) | Conf.: ±0.0244 (-0.0297...+0.0191) - [45.8%] Duration: 11 minutes 05 seconds |
|
| |
1 1296 Games rolled with Variance Reduction. Dice Seed: 7636419 Moves and cube decisions: 3-ply
|
eXtreme Gammon Version: 2.00.160.beta