STEPS
1. Open a PDF file in Skim
2. Run UIElementInspector (svailable from http://developer.apple.com/library/mac/#samplecode/UIElementInspector/Introduction/Intro.html\)
3. Highlight some text in the PDF file in skim (^⌘H)
4. Select within the highlighted text
5. Check what UiElementInspector is showing for "AXSelectedText"
RESULT
AXSelectedText is blank
EXPECTED RESULT
AXSelected Text should show the correct selected text
This works actually as expected. The selected text is in the PDF text, not in the highlight note (you cannot select text in a note). So the AXSelectedText of a note is always empty. While the AXSelectedText of the PDF text area in the situation you describe is exactly the text you selected. Be aware also that the (highlight) note is on top of the PDF text area.
Apart from that, this property is implemented by Apple, not by us.