I think I had troubles like this myself but one thing you always can check.
You did delete the exported files for your maps inside the "exports" folder aye?
If you make a map inside the map maker, that one will actually act/be your map in the game as soon as you check "has portal".
If you export this map later on for others to have, but never remove the exported files from "exports" folder, you will have 2 copies of the map automatically.
1st is the map you worked on that the game uses to read = the map folder itself inside terrains
2nd one is the actual exported map laying in exports = the same file which you send to friends.
This is usually the cause for more than 1 portal to a certain map unless it's like you mentioned above, change of name and the exporting n stuffz again.
Yeah, there's a limit on how many maps you can have, but it should be rather big.