Since they are set modal, all popup dialogs should be set to transient so it can't appear below the parent window (which makes it look like the app locked up if you have windows between the parent and the child windows). This can be done with dlg.set_transient_for(parent_widget), where you replace dlg and parent_widget with your variable names.
Fixed in CVS.
0.6.24-1
Confirmed. Looks fixed to me.