Hmm, that's pretty odd.....
First off, does the map have a ceiling? Say the spawn point is at Y=2000. If you were to put the ceiling below the spawn, say Y=1000, you would spawn under the map.
Secondly, you may have just messed up on the coordinates of the portal. Place a rock where you want the portal to be, then move to the "Controls" tab of Map Maker while the object is still selected. Take the coordinates of the object you placed and replace the already existing portal coordinates with them. After, just select the rock again and press "del" or "delete" on your keyboard (Or just go to the "Controls" tab again and click "Delete" :>)
Now when you test, you should spawn in the correct place. Hope this helped ~