urxvt
(aka rxvt-unicode) is is a fork of the well known terminal
emulator rxvt, with unicode support. It aims to be small
(smaller than xterm in terms of memory usage), fast, and
complete.
This document records some known issues with urxvt and (in the
future) other tips and tricks.
There are many causes of why this happens. The most common
reason is that you are trying to show Unicode characters which
aren't supported by the font-set that you're using. This usually
should be corrected by using the correct font-set and correct
fallback fonts.
There is one known specific issue with some (Powerline) fonts. By default, Fatdog64 uses urxvt's settings of URxvt*letterSpace: -1 to reduce the inter-letter spacing of the default monospace font (DejaVu Sans Mono), so it displays nice and tight, not wasting screen width. However, the correction may be too tight for some special fonts, such as powerline fonts, and make urxvt display boxes. Try changing -1 to 0 or even 1 to help urxvt display the special characters correctly. This will make the terminal window wider. Note: This setting is defined in /etc/X11/app-defaults/URxvt (which you can override by creating an entry in file in ~/.Xdefaults or ~/.Xresources).