Setting the primary group of a player that has not joined returns null after using this method.

Sample code? What storage type are you using?

The code for UserManager#savePlayerData is just a straightforward insert query. It definitely works for players that haven't joined the server.

Setting the primary group of a player that has not joined returns null after using this method

That may indeed be true, but it's not related to this issue. :) (perhaps more related to #1182)