I have a really weird problem here. Pinning certain apps to the superbar causes them to stop appearing in the 'frequently used programs' list - but only for certain programs; currently I've noticed it with DestroyTwitter (an Adobe Air app) but more puzzlingly, with Winamp and VLC media player.
DestroyTwitter is set to minimize/close to systray and Winamp is docked but not set to appear in the superbar at all - so its icon is always in the systray even while it's technically not 'minimized' but hidden at the top of my screen.
On the other hand, VLC doesn't have any special tray settings. Also, Digsby works fine pinned and in the recent menu, and it's set to close to systray (though it minimizes to taskbar).
I know opening an app from the pinned apps doesn't 'count' towards the use count that the frequently used programs list is based on - but even opening them from their start menu entries doesn't make any difference until I manually unpin the app. The rest of the frequently used programs list works fine.
I can't figure this out. Anyone have any thoughts? (I've tried changing the minimize-to-tray settings, with no difference).