Thank you for attaching that wiff file.
Skyline is supposed to look at all of the MS1 spectra in the file and calculate the Total Ion Current Area.
The problem is that the MS1 spectra in your file have an m/z range that the instrument collected data for in those spectra was 100-400.
Whenever Skyline sees an MS1 spectrum whose m/z range is less than 500, Skyline calls that a "SIM scan" and thinks that the spectrum is only supposed to target a subset of the precursors. This is not the right thing for Skyline to be doing in this case, since every MS1 spectrum in the file had the same m/z range.
I will ask around and try to find out if there is some way we could fix this bug. (Skyline is also supposed to use the TIC chromatogram that is already in the .wiff file, but Skyline is also not doing that, and it seems to be another bug that Skyline is not doing that.)