Hey parsh!
That message comes up every season (at game 13) as a reminder that you have to sign your free agents, even if you don't have any to sign. I handle this by...
1.) looking at renegotiation wizard to see if there are any players with 1 year left.
2.) Then I go to the team page and click on contracts. This will show you any players that were signed during the current season to a 1 year contract. These players can't be signed again until the next season.
3.) If there are no players to sign, then I click the x and dismiss the message.
It sounds like you have checked this out already, so you can dismiss the message.
I also use a sticky note and write on it, NO resigns. This helps if you are in multiple leagues and can't remember if you have signed your players already.