Regarding the issue with the retroarch squares for HUD messages, I have removed ~/configs/retroarch/retroarchcustom.cfg , yet the problem continues. What is the value that changed in this file so I can add it manually?
I am on the 3/5 build of 4.1 unstable, which was upgraded from 4.0.2.

EDIT:
Was able to figure this out by comparing to a fresh build. In the retroarchcustom.cfg file, change :
video_font_path = ""
to:
video_font_path = /recalbox/share_init/system/.emulationstation/themes/recalbox/data/ubuntu_condensed.ttf