By captured position I mean ActPos - HomePos, that is the position we see in the IDE.
I'm using AA this way: First A as 7 because we have 25 bits of data, we need to shift 7 bits to the left to have it as MSBs, it can be done using the first A as indicated in the manual. The second A is set as 2 to get the conversion from gray code to unsigned binary. I even tried using $02 instead of $72, without this shift, but get the same results, sometimes it just goes to zero (both ActPos and HomePos goes zero).
The rest is exactly as you pointed.
I tried testing changes in PowerOnMode too, do you have a guess about this parameter? It's a stepper motor and I'm using hybrid mode. I would keep PowerOnMode as 2, but I tried other configurations.