They were probably from a very old incarnation of the game that I've had sitting around for years. I tried resetting to default state from inside the game through the Options feature with no success.
I copied DOOMII and the gzdoom items over to a new directory and sure enough, there is the gzdoom-user.ini file. That's what you're talking about, isn't it? (I've included a screenshot)
How do I go about wiping the config files like you mentioned? I assume you were referring to gzdoom-user.ini?