Ok, I apologize as I know the answer is somewhere in XDA (I saw it once), but for the life of me I cannot find it via XDA's search function or google. Apparently bad search fu today.
I'm running a custom ROM that has all apps enabled for multi-window use. Which is great. But the problem is when I choose an application that is not on the first screen of apps, it will choose one from the first page instead (in I think roughly the same location of the screen). The only "work around" I've been able to deduce is on the first screen (w/o scrolling), drag the bottom right app into the multiwindow bar. Then remove it fro there. This will shift the apps up by one spot. Then repeat this until you get the app you want.
This becomes annoying when the app you want is towards the bottom of the list.
Anyone know of a better way of doing this? I recall this same issue on my S2, but perhaps I didn't have any many apps installed so it wasn't such a big deal.