Leaderless set-up, bug or not?

I noticed sometimes that when I alt tab during the game to for example IE, and then back into WoW, my alts don't all catch on and I have one or two following for example my third toon. And also not listening to the dps macro's.

Same happens when I'm in fight and I got something pop up from Windows.

I have to click all the windows from my fourth toon back through my first in order for it to restore. Obviously that's not very effective in PvP. And sometimes it's hard to see if one of my alt is cc'd or this bug happens when they stop casting in the middle of a fight.

Does anyone else with the leaderless set up has this, or anyone might have any idea how to prevent this from happening? Killing all programs apart from WoW has helped, but I got some antivirus stuff etc that I don't want to kill but can be a pain when it comes to pop ups. :<

Happens to me too.

All I do then is switch to one of them, hit my follow button then switch back to my main and carry on like normal

I have the same issue and I fix it like Jamien mentioned. I suspect this is caused by KeyClone some how losing track of window IDs or something. As in it starts sending some of the commands to windows other then the WoW clients when other windows come to the foreground. For me it happens maybe a few times a day, normally after I get IMs from people and I select the window.