How the two A and B positions are referenced in the AFCAD AND in the related SODE XML file ?
Also, assuming they are correct, there's the issue how distant the two positions are, because GSX normally use a threshold distance (I think it's 20 meters) to know where you are parked so, if the parkiing centers of the two positions are closer than that, GSX might confuse one with another but, of course, it we lowered that threshold globally, it might not have enough space to allow for different longitudinal stop positons in normal parking so, we had to find a compromise value.
There is a feature that allow a custom detection method for a specific airport and a specific gate, but it would require a customization for that airport that is not accessible to users. Assuming, of course, the AFCAD and SODE XML definitions are matching, which is the first thing to check.