Thank you for uploading that screenshot:
I see that the same filename has been repeated 17 times in the "Extract Chromatograms" part of the Import Peptide Search wizard. I am not sure why Skyline would do that.
We will actually need a few more files from you in order to reproduce this.
In addition to that "msms.txt" file, we will also need your "mqpar.xml" file, and, if you have them "modifications.xml" and/or "evidence.txt".
It would also be helpful if you could zip up "1.AD1-2_S1-A2_1_9348.d" and "2.AD17-7_S1-C4_1_9384.d" and upload those too.
Also, if you could send us your Skyline document (even if that Skyline document is blank), that would be helpful too.
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 and spectral libraries.
You can put all of those things into one big zip file and upload them here: