I used to have it, but now it's gone. I think I fixed it by (accidentally) installing Zero-k twice. I installed it to C:\Users\Flipstip\Documents\My Games\Spring and to C:\Users\Flipstip\Documents\My Games\Zero-k.
The installation in \Spring doesn't have the pop-up, but the one in Zero-k has it. But don't ask me why. (In case you're wondering why I keep the installation in \Zero-k, sometimes when Zero-K lobby breaks due to some update, I can fix it by starting up the other copy of the lobby)