Malformed stroke when creating layers from layer styles

My first and second images show a Layerset with three layer style strokes applied to the Layerset group.  The larger square is inside the set and the smaller one is outside the set.  The first image shows how the strokes appear before right clicking on the layer styles and selecting create layers from the menu. The second image shows the result of doing this.  All strokes have become layers and look the same as they did before making layers from the layer styles. This is how it should be.

In the third and fouth images both squares are inside the Layerset at the same time.  The fourth image shows how they look when layers are created from the layer styles.  They no longer appear the way they should. 

The point I'm trying to convey is that creating layers from stroke layer styles on a layerset with more than one artlayer in the set results in malformed layers for strokes where the position of the stroke is set to center or outside.

I do spot color separation work and use this technique quite often to get a clean separation of colors on artlayers with layer styles applied to them.

@bhales1 

Your first image shows that the only thing in Group 1 is 3 strokes (Effects).

 This image is more confusing. Group 1 has 2 rectangles in it and no Effects.

• Above are layers called "Inner strokes" that are not Effects and are clipped to group 1.
• Below are layers called "Outer strokes"

I'm not sure what you are trying to achieve, but consider applying multiple Strokes as Effects to one shape, and format each stroke with the color and width. If you accidentally have a thick stroke hiding the thinner strokes, you can drag to reorder them.

Show us a screenshot of one shape with the Effects panel > Stroke so we can see what you have.

Jane