I've found the solution to my problem, thanks for all of your input.
It turns out, upon unzipping the game's .pk3's to my /gamedata/base/ directory, it placed a /textures/system/ folder in there that contained only the security code textures. When JK2Radiant was executed, it was looking for /textures/system/, found those, and decided not to load the default textures it understands to be in /system/
What I did to get around this: I simply renamed the /textures/system/ folder I had to /textures/system2/ so as not to override the default system textures for JK2Radiant. When I entered the program again, the textures pull down had put in its own system textures, and one of them was thankfully origin.
Thanks all, hope anyone with the same problem finds this post. =)