Ok so from what they have said previous your free company can align itself to one grand company. This will let you do things with that grand company that you would normally not be able to do because that grand company wasnt your grand company.
The thing is, there are three grand companies and only two you can be a part of (1 from FC, one from yourself).
So assuming a perfect distribution of players chosen grand companies (1/3 to each company) when your LS goes to make a FC and align itself to one GC.
Bob is a part of imperial flames IF
Tim is a part of the Twin Adders TA
and Jake is a part of the Maelstrom (?) M
Your FC decides to align itself with TA. Bob and Jake get to use a new GC. Tim is not going to get anything new (TA + TA = still TA).