Can you post a screenshot of what you are seeing? I am not sure that I understand your question.
If you would like, you could send us your Skyline document and your .mzXML file and we could take a look.
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.
If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
https://skyline.ms/files.url
You can also send us your .mzXML file.
Skyline knows how to read Bruker .d raw file directories, so it was probably not necessary to convert them to mzXML. If you would like, you could zip up one of your raw files and send it to us too.
-- Nick