I'm using windows via Bootcamp or Parallels, and just recently when i use any applications on windows in full-screen [Maximize button] (e.g. Chrome, Adobe CS), the full-screen takes up the whole screen even going over/under the windows taskbar. Screenshot: http://cl.ly/230e0f0Y2E2U302p3c2x Here you can see chrome browser in full-screen under the taskbar. Not sure how it happened, but only started shortly after installing Parellels on mac and connecting my bootcamp to it.
The only way I could reproduce this was if I turned off "Auto-hide the taskbar" in the Win 7 taskbar preferences and then maximized a window. If it happens whether you've booted from BC or are running Parallels, then it must be a Windows setting, not any fault of Parallels. Steve