So, I have Geany\share\gtk-3.0\settings.ini and Geany\share\themes\win32mod\gtk-3.0\gtk.css and here is the result:
Well, no idea what may be wrong (I don't have access to a Windows machine right now and won't have it in the following two weeks so I can't test anything). But did you also delete the theme-setting stuff under `C:\Users\Name\AppData`?