The issue is the icon /usr/share/icons/hicolor/48x48/apps/gbrainy.png is actually a 32x32 icon.
The bug appears to be in data/Makefile.am as it installs data/app-graphics/gbrainy.png into the 48x48 dir. Guessing you need to make gbrainy32.png and gbrainy48.png.
The issue is the icon /usr/share/ icons/hicolor/ 48x48/apps/ gbrainy. png is actually a 32x32 icon.
The bug appears to be in data/Makefile.am as it installs data/app- graphics/ gbrainy. png into the 48x48 dir. Guessing you need to make gbrainy32.png and gbrainy48.png.