We recently found that it's possible to come across negative counts in PE NetCDF files. We created a workaround for this by importing the .xl files using iolite's General Text importer (in the Tools menu). The .xl files don't have timestamps recorded in them, so you have to manually enter a time for each file, and you can only import one file at a time.
Thankfully, Tephy Marillo-Sialer at PE worked out what was causing the issue. Exporting the data using a "Data only" method will result in data with no detector calibration applied (hence the negative counts). You need to ensure you're using a Quantitative Method for export.
If you have any questions about getting your data into iolite, I recommend checking out the Perkin Elmer section in iolite's documentation and in particular the pdf guide that you can download from there: