Question about Themes and Wallpapers

I've come across an interesting frustration. For the longest time I had one particular theme installed. I have since deleted it. I applied the default theme. Then I applied a wallpaper.
I now have the old icon tray (the customizable ones by the all apps icon) behind my current icon tray. If a wallpaper is not applied, then it's not visible. When it's behind my app tray it is not functional, and I wish I could ignore it, but it thinks there's a notification.). And it is visible on the background when it let's me select a wallpaper.
Any ideas?

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Question about Themes and Wallpapers