Well, i just tried on a fresh install of Retropie v.3b4 and … the behavior is the same : runcommand.sh line 671: 3034 Segmentation fault.
The steps i did for this install :
* Write the image on SD card
* Detect my pad with emulationstation (/opt/retropie/configs/all/retroarch-joypads/USB,2-axis_8-button_gamepad__.cfg generated)
* Add “Alex kidd in Miracle World” (all my childhood :D) in mastersystem roms directory.
* Edit the retroarch.cfg in mastersystem in order to enable shaders (with and without the 1st line):

video_shader = /opt/retropie/emulators/retroarch/shader/phosphor.glslp
video_shader_enable = true

* Edit USB,2-axis_8-button_gamepad__.cfg : i tested 2 configs :

/* other buttons... */
input_shader_prev_axis = "-1"
input_shader_next_axis = "+1"
input_enable_hotkey_btn = "6"

and

/* other buttons... */
input_enable_hotkey_btn = "6"
input_shader_prev_axis = "-1"
input_shader_next_axis = "+1"

I swapped +/-0 and +/-1, same result on the respective shader assign button.

The complete log file : /tmp/runcommand.log

RetroArch: rarch_log_libretro: [libretro INFO] :: detected SMS ROM

RetroArch [WARN] :: resolve_extensions :: [GL]: GLES implementation does not have BGRA8888 extension.
32-bit path will require conversion.
/opt/retropie/supplementary/runcommand/runcommand.sh: line 671:  4442 Segmentation fault      /opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-picodrive/picodrive_libretro.so --config /opt/retropie/configs/mastersystem/retroarch.cfg "/home/pi/RetroPie/roms/mastersystem/Alex Kidd in Miracle World (UE) [!].sms" --appendconfig /tmp/retroarch.cfg