Yes, please send us your 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.
The Share Document dialog gives you the option to include the raw data files in the .zip, which would be a good thing to do.
Alternative, you could zip up your Bruker .d folders in a separate .zip file and send them to us.
You can upload your files here:
https://skyline.ms/files.url
After we see your Skyline document and your Bruker data files we will be able to tell you why Skyline is doing what it's doing.
-- Nick