Thanks for all the help guys
I worked it out thanks to a reply in another thread...
For anyone that searches and finds this thread looking for an answer, I'll post so you know
You have to change the nation thats teams are being put into the new playable League (or the bigger league etc) to have the three letter abbreviation of the nation that you are changing from.
So in my experiment, the A-League is a twelve team, two tier league, based on Israel league.
The New Zealand Leauge is an 8 team league based on the 8 League.
So Australias 3 letter abbreviation becomes ISR (this was Israels), New Zealands becomes AUS, and Israels becomes NZL.
Im guessing the game engine uses these three letter abbreviations as flags, or as unique IDs for these nations