This problem has been around since the beginning of eCabinets
I want to use front and back top stretchers in base cabinets across partitions with top full dado joinery to easily position the partitions.
when you do this in eCabinets only one of the top stretchers get the full dado cut.
It is the same problem if you eliminate the top and manually place left /right stretchers (front/back orientation) as the top, only one stretcher will get the dado cut in it.
It is something we are aware of, but not able to implement any type of reasonably easy fix. I'd suggest using a phantom stretcher with insets associated to the partition to create the second construction. We are aware how much of a pain that is, and would like to fix sometime in the nearer future, but here we are.