Your scenario is not that clear, but I think you have custom dropdownlist with checkboxlist as DropDown values and when you open the values area its behind other controls.
Well if it is a custom control, you need to set the the
z-index
CSS property of the DropDown values control (either its a div or panel etc.). Set it to a higher value
z-index:5000;
and test.
Let me know if it helps, or if not please provide me more clear info, may be a little code.
Good luck
Azee...