When you activate Model Builder, it sets all layers to a certain transparency (75% by default) - in certain circumstances ARD doesn't restore the layers to 0% transparency.

Layers with transparency appear dim (or dark, on a black background).

You need to open the Layer Manager and look at the Transparency column. If they are all set to 75% then you need to highlight all the layers, click in a cell under the Transparency heading and type zero.