It is quite common for the cubeful equity describing the move made on move n to be different from the cubeful equity given by the cube analysis at the start of move n+1.  On rare occasions the discrepancy can be large (>0.25).  The discrepancies are associated with different pruning. I have the analysis level set to 4-ply, and the cube decision always reports the 4-ply numbers.  But the checker play often prunes to less than 4-ply.   
When I go to the advanced settings and turn off "use neural net pruning" for both cube decisions and checker play, the actual pruning reported for these decisions does not change.   Does this mean that pruning is still used, but using a different method than the neural net?   Or I have misunderstood what these checkboxes mean? Or is the request failing to register?

The attached game shows an example at Blacks move 15.  The equities for the moves are all pruned to 0-ply, even if "neural net pruning" is turned off in advanced settings (and clear and re-analyse the move).

(BTW, despite this minor issue, gnubg is a wonderful tool that I love!)