Most likely, you're looking at a path problem to the Excel file from the applicaiton.
When you build a VI into an applicaiton, the path to that applicaiton changes. If originally the VI that calls the Excel file was located "c:\app\caller.vi", after you build the executable, that same VI will now be located at "c:\app\toplevelVI.exe\caller.vi".
The executables name will now actually be a part of the path. So you may need to add an extra "Strip Path" function somewhere to get you to the real path to the Excel file. Of course this is just a guess without seeing your code. You could try going back to the LabVIEW code and add a path indicator where you are building the path, then re-build the application and run it so you can see what the path is after it's built.
Ed