I'm having the same problem. My tiles in the metro start screen are all the default MS skittles colors after the 8.1 upgrade, regardless of what's set or selected in Decor8. The function where Decor8 would choose a unified color scheme for the tiles based on the selected background was working perfectly in Win 8, but something in Win 8.1 seems to have broken that feature. The Decor8-determined color scheme only applies to the start icon in the pop-up sidebar now, and the sidebar overlay itself is always just black.
I don't really care so much about the sidebar overlay, but I recoil in horror every time I enter the start screen now due to MS's random garish tile colors.