Not applicable as the problem persists in the new user's account.
Darn, I was kinda expecting this but hoping new user will solve the problem.
This means that it's a system config, /usr/local/share/... of some sorts probably, Maybe someone else who has his fingers deeper in customization can land a hand here, sorry to say i'm out of ideas except the obvious, format, reinstall
By the way, similar thing happened to me some months ago where I bork-bork-borked my system so that actually gnome-panel would read one theme config file, every other gtk app another, so basically I could apply two different themes. To this day I have no idea what did I do, but one thing in common with your problem was that I tried a lot of times to apply settings using all bunch of different tools. Anyway, my whole system was kinda bad so I did a reinstall later on and used only the systemsettings+lxappearance combination with the qtcurve and all i well since.
Anyway. stick around, maybe somebody will offer different perspective. Good luck, man.