Well the cooldown is 2 seconds. I'm not certain if the 20% attack speed buff has to go down before this cooldown is engage (though I assume it would since the 4 second AS boost doesn't stack to my knowledge). So that would imply that a minimum 6 seconds between WBL procs.
Unless of course you are simply referring to games where the mastery fails to work at all. Similar things are happening with Thunderlord's Decree in which only one instance of the keystone works if more than one person on a team has it. By your description it sounds as though you are editing your runes/masteries during champ select and perhaps they are not saving in time for you to begin the game. Likewise, if you attempt to switch rune pages or summoner spells right before a game starts then these changes won't be applied. If that's the case then try not to wait until the last second to change your masteries.
