Problem with 2D annotation layers

[EmilieTeo]

I'm using Juicebox 1.11.08, when I load a .assembly file and then a .bedpe file as 2D annotations, I don't see the annotations contained in the bedpe file. Even when I'm using the arrows in the annotation panel to put that layer in the front, nothing happens. The only way to make them appear is to merge the layers, but then I can't do any modifications to my scaffolds.

To load the bedpe file, I'm going to the 2D annotations tab in the annotation panel and click "Add Local" to select my file. I get the following annotation panel but the purple layer is not visible.