Ok, let's keep this short. Flat Map: And "Surface" Map: What the heck! Help me! Look at it for yourself, mc.mdzserver.com:8123
This is actually kind of normal unless you do a full render of a map at some point to "catch it up" to the current state. Check inside the dynmap configuration file and see what it is using for the update triggers. If too many of them are turned off then it simply won't render your map.
If it does not solve the problem, you might have to delete your tile folders for the broken maps and just re-render them fully from scratch... however I suspect just doing a fullrender should work for this one. Fair warning, it might lag you for a bit while it does it's thing.
Its like a strategy game, you have to explore the dark places to revel the land had the same thing before, and I flew around the dark bits, and it rendered them. :3
Even then, depending on what triggers he has set, this might not even work. Even this method relies on something changing to cause dynmap to update that tile.
Ahhh right. When I had it I just flew around and it rendered, didn't have to configure anything other than what IP & port it binds too