I had this very annoying problem in Windows XP (SP2). When I hovered mouse over a tray icon to show it’s tooltip, the tooltip was showing behind taskbar. I don’t know if there is an official fix to this issue but the following worked for me:

1. Open regedit (Start–>Run–>regedit)
2. Go to the following key:
HKEY_LOCAL_MACHINESOFTWAREMicrosoftWindows
CurrentVersionExplorerVisualEffectsTooltipAnimation
3. Create (Right Click–>New–>String Value) or modify value:
   SetWindowPos=HwndInsertAfter, Hwnd_Top
4. Create (Right Click–>New–>DWORD Value) or modify value:
   SetForegroundWindow=1
5. Restart Windows