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