That font looks like the odd default fallback of urxvt if the font name provided can't be matched.Did you rebuild your font cache after installing terminus?EDIT: Deleted some irrelevancies since I am still learning to NOT read commented out lines of files.
I suspect there is something wrong with your xresources. Update fully (pacman -Syu), then remove any settings from .Xresources/.Xdefaults, restart X to make sure you have a clean resource database, then try launching urxvt.
By "true transparency" I assume you are using something like transset-df rather than urxvt's own rgba settings, right?Pseudotransparency copies the wallpaper to the urxvt window background.Transset-df style transparency makes the entire urxvt window partially transparent - so this includes the text.Urxvt's own transparency makes only the window background transparent while keep
I've never used subtle, but I suspect it identifies client windows (for putting them on selected tags) by their resource name/class. You can easily set these when you start urxvt (e.g. with the -name flag) so you can have different resource names for different urxvt windows.
Two of those window are vim. Are you using vim? Have you turned on syntax highlighting?What have you done with your Xdefaults? There isn't much you can do there that is relevant to this other than defining what the 16 base colors will be - redefining these colors does not make any program use them.
Ok solved. urxvt-fullscreen places the perl files into /usr/lib/urxvt/perl/fullscreen but reading urxvt man page it seems that URxvt does not look for extensions there, but rather in $HOME/.urxvt and /usr/local/lib/urxvt/perl. Symlinking the perl file into ~/.urxvt/ext solved the problem.