Hi Jeremy,
We had the same problem, it took us a while but we think we know what is causing the issue. When you click the "Analyze" button before you share the map, the "Prepare" dock window will appear and clip off the bottom portion of your map. (The Share As > Runtime Content takes your current map display extent to clip your map). Even when we close the Prepare window or avoid "Analyze" prior to Sharing, we find that this Prepare window can still pop up and immediately hide itself. But I guess there's still timing issue where sometimes it will clip the map and other times it doesn't.
We find that the best way to avoid the clipping is using the "Create Runtime Content" tool. Hope this helps.