Adding a pattern to Swatches then getting a different Pattern when Filling

I make patterns for an apparel company. Have made hundreds of these patterns. Today, I added a patternt to the swatch panel looking exactly how I want it. When I add it to fill the mock up the black sleeves of the artwork jump up front!! I cannot firgure out what happened. I tried this with a pattern I know work and now that is layering backwards as well. Any help is greatly appreciated. Screenshot should help explain this better than this post....