I certainly thought that the ranks would be exactly as you would expect: you sort the transitions by the peak area that they have in the currently selected replicate, and the number in square brackets is the position of the transition in that sorted list.
There are things that you can do which might confuse Skyline and cause it to display incorrect numbers. If I delete a transition and then do "Edit > Undo", the rankings displayed end up being incorrect (and there are some duplicate numbers).
If you exit Skyline, and then start Skyline again and open the document, are the numbers still incorrect?
If you would like, you can send us your Skyline document and I might be able to give you more information about why Skyline is doing what it is doing.
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.
You can upload larger files here:
I will also send you an email directly in case you want to send your Skyline document to us privately.