You should go to the "Instrument" tab at "Settings > Transition Settings" and uncheck the box that says "Triggered chromatogram extraction".
That checkbox would be used if you were doing something like a Thermo SureQuant method where the mass spectrometer has been told to start collecting spectra for a particular precursor as soon as something else is observed.
When the box is checked Skyline has heuristics for figuring out over which time intervals data was not being acquired.

You can find more information about that checkbox here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=TriggeredAcquisition
-- Nick