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A small amount of weight / authority will be lost when changing the URL's and 301 redirecting to the new locations. It's only fractionable but could be the difference between 3 or 4 positions in the search results within your niche. It's possible there could be an issue with the 3rd party plugin you used, they may have overlooked something critical in this process. When did you notice the drop in rankings / traffic? Is it possible it could also be due to Panda/Penguin preparation/updates also?