If Skyline has extracted chromatograms from both MS1 and MS2 spectra, and Skyline notices that the extracted MS2 chromatogram covers a shorter time range than the MS1 chromatograms, then Skyline will truncate the MS1 chromatograms so that they are the same length as the MS2 chromatograms.
The reason that Skyline does this is that it is the correct thing to do in scheduled PRM experiments.
That is the most likely reason that your MS1 chromatograms are truncated like that.
One way to prevent Skyline from doing this would be to go to:
Settings > Transition Settings > Full Scan
and change the MS/MS Acquisition Method to "DDA".
When the MS2 acquisition method is "DDA", Skyline will not truncate the MS1 chromatograms, but also, Skyline will treat the MS2 transitions as "Non quantitative" and their chromatograms will be drawn in dotted lines.
It's possible that something else is going wrong.
If it does not seem that your matching MS2 spectra cover a different time range than the MS1 spectra then you can send us your Skyline document and one or more of your raw files.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
Files which are less than 50MB can be attached to this support request.
You can upload larger files here: