The ratpoison window manager seems to have some kind of weird issues with urxvt and borders, or the other way around. The right and bottom border of a window gets 1px thicker than the rest and I can’t seem to figure out why. I’ve recompiled a clean urxvt and tried different fonts, grepped the ratpoison source and investigated window manager hints, not to much avail.
Since the borders are merely for aesthetics I found another solution:
By using the gap feature introduced by jcs:
set gap 1
together with no border in Xresources, we can see 1px of the background inbetween the windows. Since the background is black (by default), just change it to your desired border color like so:
xsetroot -solid '#ff5400'
and we get perfect borders as a result: