Can you send us one of your raw files that is having problems? You can zip up the .raw folder and upload it here:
https://skyline.ms/files.url

It would be interesting to check whether this problem also happens with ProteoWizard SeeMS.exe or MSConvert.exe.

If you think this might be a Skyline-specific problem, then you should also send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.

-- Nick

I've uploaded the files and will try to use the other programs today.

Thank you for sending us those files.

The error is happening when Skyline is trying to get centroided spectra. You can work around this problem in Skyline by going to:
Settings > Transition Settings > Full Scan
and change "Precursor Mass Analyzer" to something else (anything other than "Centroided").

I will ask around and try to find out if someone can fix this bug.

-- Nick

Thanks Nick.

Changing the Precursor Mass Analyzer did fix it.