OK so this was a combination of multiple issues.
1. If your chocobo is stabled and you have "Use Mount" enabled you will simply never move.
2. I didn't have ignore marker levels checked.
So it's working now however the nodes I want it to farm from are level 25 and it keeps running to the level 30 ones. I tried editing the marker and then saving the nav mesh to make the other level 25 nodes higher level however after I save the mesh it seems to reset the marker and it says 21-25 again.
1. If your chocobo is stabled and you have "Use Mount" enabled you will simply never move.
2. I didn't have ignore marker levels checked.
So it's working now however the nodes I want it to farm from are level 25 and it keeps running to the level 30 ones. I tried editing the marker and then saving the nav mesh to make the other level 25 nodes higher level however after I save the mesh it seems to reset the marker and it says 21-25 again.