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.
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.