I’ve been having the same issue. I also switch the buttons on my PS3 controller for GB and NES like you do.

In both /opt/retropie/configs/nes/retroarch.cfg and /opt/retropie/configs/gb/retroarch.cfg I add the following lines. These two lines are the only edits I made to those files.
input_player1_a_btn = “14”
input_player1_b_btn = “15”

In my /opt/retropie/configs/all/retroarch.cfg those buttons are assigned as follows:
input_player1_b_btn = “14”
input_player1_a_btn = “13”

But for some reason it doesn’t pick up the new button remappings. Any ideas?
I recently upgraded to 2.6 on a RPI2, but I never had this problem in 2.5/RPI1 B+.