I have solved it!

On another thread I found about the hidden .emulationstation directory. I then found the es_systems.cfg file and was able to change where the gameboy and other retroarch emulators are called.

In the regenerated file it tries to call retroarch from /home/pi/RetroPie/emulators/RetroArch/installdir/bin/retroarch

By removing the /installdir/bin from the command the emulator will start correctly. :-)

Out of interest if I reorder the emulators in this file will it be in that order in ES?