That Agilent external tool reads through your Skyline document file (.sky) in order to figure out what modifications you have defined.
It sounds like the tool is getting confused about the same modification appearing twice somewhere.
I imagine that this might happen if you have the multiple heavy isotope label types at "Settings > Peptide Settings > Modifications" and the same modification is associated with more than one Isotope Label Type.
If you would like, you can send us your Skyline document. I can send that to the people I know at Agilent and make sure that they know about this bug.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.
If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
Are you using the MPPReport from the Skyline tools store, or did you get that tool from somewhere else? If you got it from somewhere else, can you send me the .zip file that you used to install the tool in Skyline?