While going through my settings I wanted to try out the "dark menu bar" in the General System Preferences. Now I cannot turn it off. Each time I uncheck the checkbox, it seems to have no effect, it's stuck in dark mode. I've tried booting into Safe Boot as well to see if i could change it there, to no avail.
This seems to also only be for my user, as switching to guest mode works properly. https://www.youtube.com/watch?v=h6Ga6bXEFEo
Screencast of the issue: https://www.youtube.com/watch?v=xNEHhoFzniI
Machine: OS X El Capitan 10.11.16 MBP Retina 15, Mid-2015
Edit: replaced screencasts with jing to youtube so that non-flash users can view the issues