I much prefer the popup, as it's one click. About half the time it's not a popup, but a message stating so and so wishes to join you. Then you have to use the .accept "XYZ" command.
I have a feeling it has to do with how they tried to join you (typing .join vs. right clicking your name on roster and hitting 'join' etc)
Is there, or can there be a way to setit so you get the popup etc.?