ok, there is a fix for this..
so start yer Pi as normal,
then when the EmulationStation config screen pops up, assign the buttons as well as you can.
next you need to set your retroarch config via the ES RetroPie menu. once that is done launch the RetroPie SetUp script.
now you need to select #3 Setup / Configuration (to be used post install) then scroll right down to the bottom if the list, select #331 Install XBox contr. 360 driver
now reboot.
now ES will ask you to assign the buttons again, and now the trigger & shoulder buttons should register