well, and it depends on how you adjusted you popup behavior.
Often, you have 2 or more pops for diff. IPs, diff. ports, diff. direction, diff protocol.
If you, for example have adjusted to the highest possibility, you sure have to click every single popup.
I think important to understand is, that the popup behavior options, only hide popups if there is already a rule. And the kind of rule that will be created depends on the adjustment.
So if you have adjusted to “only one pop for an app” (eg no direction, no port,no ip…), at the first time the app is trying to communicate you will get all specific popups anyhow !!! But in this case, if you click on the first, all will close. (That is, because a rule for App X, any,any,any is made, and with that the other popups are no longer important (all is already allowed).
So a tipp: if you try to configure an app for specific things, its best to adjust the popup behav. to highest, or at least so high, that you get the specific rules you want. After that, its much easier to make the rules complete, if it is necessary at all.
( I hope this is all true, but for my testing it was)