Is this topic too old to answer? I've been messing with this all day and I think I found a solution. My server is a single cell, and I placed 11 islands in that cell as well as 3 freeports. Everything I tried including setting the freeport islands to 0,1,2,3 and the rest to -1 didn't work.
In the Spawn region to the right of character creation I see island (1130), island (1131), no idea where these numbers are coming from. It would be cool to see some kind of name here.
So I tried something screwy. I started with the freeport islands and set them all to be spawn points, starting with 0 and going up to the last island. And it worked! When I choose the first island in the list I'm at freeport #0.
I also tried the bAutoGenerateIslandSpawnRegions=false which did no good in either the default gameusersettings.ini or in the save at 00
Edit: Just reied choosing the second island in the list and wound up at freeport 1, yay!