I've been using the Alit theme for a while, but felt like disabling it, however when I disable it, them apps which it dosen't use a custom icon and replaces the layer over it stay in the themes style, ive even tried deleting the Over Images from the theme itself in SSH but no prevail, ive had this since using 3.1.2 using Blackra1n.
Also for some reason the theme and winterboard are not appearing in Cydia's installed list, and I manually removed Winterboard but still the icon problem, the icons in the app store are fine.
So it currently looks like this
