Could you please share your font configuration? A screenshot from gnome-tweak-tool will do. Have you done some modifications to gtk theme? I just downloaded Adwaita Cupertino and there are some diferences mostly in side-panel, the window manager theme is different also.
Here is the font configuration: [link] Yes i have modified the gtk theme, try this one ([link]) i heve modified this.. The one i am using now it is not finished yet.. when it's ready i will publish it..