Make sure you have the enclosure names specified that you want to see in the map. The FM Server map relies on enclosure names. If you use device aliases (or even FC aliases), there is a button in the FM server information pane that will let you apply the alias names to the enclosure names.
You can also just type in the enclosure names, and then click the 'apply' button. Once you have the enclosure names listed correctly, rediscover/refresh and your map should look more like what you expect.