I know this is not what you want to hear, but you need to close all references. Unless there is an error in the chain that is preventing the Quit command from executing, Excel should close properly.
Go back and look at all subvis make sure that every reference that does not leave the vi is closed in the vi. All references that are brought out must be closed somewhere else.
Otherwise, try to skip some of the Excel functions in your program and see if the problem disappears. Try to close the current Workbook before quitting to see if that happens correctly. You can also use the OpenG toolkit to try to close the application by window name.
Michael Munroe
www.abcdefirm.com