I've been able to replicate the problem with a reasonably straightforward case.
Using a freshly downloaded ebook from O'Reilly, Head First iPhone Development. That file reports that it was created by Adobe PDF Library 9.0 and Adobe InDesign CS4 (6.0). My steps were:
* went to logical page 37 (chapter 1 page 3).
* selected a line of text that read "ported desktop apps"
* copied; SUCCESSFUL
* annotated that line with a highlight
* selected "ported desktop apps" again
* copied; SUCCESSFUL
* saved
* selected "ported desktop apps" again
* copied; SUCCESSFUL
* select the first occurrence of the word "about" on the page
* annotated with a highlight
* selected "ported desktop apps" again
* copied; SUCCESSFUL
* saved
* selected "ported desktop apps" again
* copied; FAILED!
The results of each copy can be seen in this screenshot showing iClip's contents (last at the top; first at the bottom) after each copy operation:
http://dl.dropbox.com/u/1184374/resultsOfCopy.png
I was NOT able to replicate the failure in simple PDFs that were generated from
(a) TextEdit using Lorem Ipsum text, (b) in Acrobat 9 Pro creating a PDF from a webpage [yahoo.com], or (c) in a PDF created from Firefox from a webpage.
-Wil