@Blueblood: the reason why your problem is happening it's quite obvious; solving it is something different, though. When you grant indipendence to your colony, they also "start as minor civs", exaclty like you did when you started the game. So they are of course at war with everyone. I'll have a look to the code in order to modify this. @IPEX: that might be, I'll have a look at this too; but I think the error could be somewhere in the code for minor civs. Thank you for your report.