Glad someone can confirm this. Unlike you, I am unable to reproduce it with applications I opened manually though.

Test: I open Winamp over mIRC. Highlight of the active switchbar item in mIRC is removed if I...
- close Winamp
- click on its taskbar button to deselect it
- select mIRC in the windows taskbar
- reactivate mIRC by clicking into its window
- jump to mIRC using Alt+Tab

Win XP Pro SP2