When Skyline is extracting from a file which has both regular MS1 spectra and SIM spectra which match the precursor, Skyline will preferentially extract chromatogram points from the SIM spectra. In Skyline, a SIM spectrum is defined as any spectrum where the m/z range that was scanned is less than 500m/z.
Sometimes you would prefer that Skyline extract chromatograms from the MS1 spectra instead of the SIM spectra, in which case you should check the checkbox "Ignore SIM scans" at "Settings > Transition Settings > Full Scan" and then reimport chromatograms using the Reimport button at "Edit > Manage Results".
When Skyline extracts chromatograms from spectra, Skyline sums the intensities across a m/z channel centered on the target m/z. The width of the channel that Skyline sums across is controlled by the "Resolution" setting at "Settings > Transition Settings > Full Scan".
If you click on a point along the chromatogram Skyline will bring up a spectrum viewer which will display the spectrum from which that chromatogram point was extracted. The spectrum viewer will highlight the m/z channel that was summed across.
If the chromatogram that you see is completely flat, and you expect there to be some signal, the problem might be that the extraction window was too narrow in which case you should choose a lower resolution at "Settings > Transition Settings > Full Scan" and then reimport chromatograms using the Reimport button at "Edit > Manage Results".
By the way, it would be very helpful if you could send me "Pos_CC6.d". I am confused by what I am seeing in terms of what Skyline thinks the spectra looked like in terms of what m/z range was available. If I could see your original raw data I could figure out whether there is a bug here that I need to fix.
You can package the "Pos_CC6.d" folder in a zip file. If that zip file is less than 50MB you can attach it to this support request, otherwise you can upload larger files here:
https://skyline.ms/files.url
-- Nick