I hit this one twice in one week - small molecule users were confused that the Library Match window was empty even though they knew the molecules in the Targets window could be found in the library. Had to explain that it only works when the library is the basis of the Targets list, but that is not intuitive to them.

You'll have to explain what you mean. This makes it sound a little like small molecules are not matching to library spectra correctly. The concept of "populated from" is not really meaningful in the peptide world. If you put a peptide precursor into a Skyline document, no matter how you add it, if it matches spectra in the libraries associated with the document, all of those matches should get listed and presented by the Library Match view. If that isn't happening on the small molecule side, that sounds more like a bug in the small molecule code than a usability suggestion. Even if none of the fragment ions match the library peaks, the precursor should still match the library (and show that by the mini spectrum in the precursor icon). In the peptide world, I am not quite sure how you would have anything useful to show in the Library Match view when the precursor icon is not showing a mini spectrum, indicating there is a library match.