Make sure you only have one Sapphire skin subscribed/enabled at a time. I use the Silicon skin and it works pretty well - sometimes I have to "reload active skin" to get certain mod-specific icons to appear, but on the whole it's much improved UI.
There is also issue that the game's current UI code seems to have been written in a great rush, it's shockingly bad. Like icons on the menus are 109x100 (from vague memory), but you can only use 109x75 - why? And one of the icons must always be in "selected" state - why? There should be decent and reliable ways to create windows, nice looking graphs (not the ugly things currently provided), add buttons and so on. It needs a vast amount of refinement. I'm not surprised that the Sapphire skins are mostly "on hold" (probably abandoned) with the current state of the vanilla UI system. IMHO the whole native UI needs an overhaul to something that works much better, but that will probably kill the Sapphire skins dead, so it's not looking good whatever route is taken