What I am doing is, I open up a file I saved as an Illustrator template, which I have used several times to create icons. What's happening is, I created a rounded rectangle and set it for a 2px stroke, but no fill, yet Illustrator is filling it with this off brown color. Why is that?
As previously commented the layer "Layer 1" has an appearance override. You can see this because the circle next to the name is filled. Click on the filled circle and clear appearance in the appearances panel and you are clear of the effect.
Note, slecting a item in the layers panel does not select the object unless you click on the circle.