This is probably a question for the Skyline support board. But I do believe that whether Skyline calculates mass errors or not is determined by the settings in Skyline. I downloaded the latest .sky.zip files from your AutoQC_BSA_Fus folder and one from the AutoQC_BSA_QEx folder. One difference in the settings that may determine if mass accuracy is calculated or not is the precursor mass analyzer selected under "Transition Settings" > "Full-Scan" > "MS1 filtering". It is "QIT" in the Skyline document where you don't see mass errors, and "Orbitrap" in the other one. My guess is that Skyline does not calculate mass errors for a low resolution mass analyzer (QIT). Do you have a high resolution mass analyzer selected in your other documents where you see mass errors?
Just for future reference, it will be great if you can point me to the URL of the Panorama folder where you have questions. It is easy for me to download a Skyline document from a Panorama folder, and I need a shared zip file (*.sky.zip) anyway so that I can see the chromatogram data. Chromatogram peak data is not included in the .sky files. It is stored in the binary .skyd files which get included when you create a shared zip archive either for uploading to Panorama or from the File > Share menu.
Thanks a lot!