Hi Andrew,
Thanks for providing the example file. I find that it can't be opened with msconvert nor SeeMS, which means it's either damaged or some format variant that isn't supported by the ProteoWizard library. I rather think it's damaged, since as far as I know the only Agilent formats we don't handle are those that are from Chemstation, and this doesn't seem to be that kind of data.
Are you able to open the file with other tools?
Thanks for using the Skyline support board,
Brian Pratt