The "mirror" option in the Library Match window allows you to compare a spectrum in your spectral library (.blib file) with a spectrum which Skyline gets by asking the Prosit web server for a spectrum.
It sounds like your spectral library .blib file was generated from Prosit, so, yes, you would expect the top and bottom halves of your mirror spectrum to be identical.
It sounds like you would like Skyline to instead be showing you a spectrum from your raw file. I cannot think of a way to get Skyline to do that for you.
If you want to see how your chromatogram peak areas compare to the intensities in your spectral library, you can use the menu item:
View > Peak Areas > Replicate Comparison
The peak area replicate comparison graph will show you one bar representing the intensities from the spectral library, and it will also have other bars for the replicates in your Skyline document.