After much research at https://github.com/Neverball/neverball/issues/170, it seems this issue only affects the Debian package for some reason, likely a weird compiler bug or such. Anyways, the solution seems to be a rebuild of the package. No changes are needed, just re-compiling seems to fix the issue. If a maintainer can do this, the bug can be closed.
- Bug#871223:  neverball: Strange squares instead of... Qwerty Chouskie
- Bug#871223:  neverball: Strange squares inste... Markus Koschany