Hi,
I am not sure about the flickering, but if it is now opaque and you are using windows vista or windows 7, right click a blank spot on your desktop and choose personalize. In the window that opens, at the bottom there is an option that says window color. Click that and on the window that opens, there is an option that says enable transparency. If that is unchecked, it will make your taskbar opaque. Check the box and that should make the aero glass effect return on the taskbar. Flickering could be caused by the refresh rate on your monitor if you have a CRT monitor, or it could be a problem with the backlight if you have an LCD.