Paula. I have always found this to be the case—Acrobat and Acrobat Reader can find word breaks that Skim and other apps that use Apple's software cannot. Try opening your pdfs in Preview and seeing if you get the same behavior as in Skim—I bet you will. Perhaps someone can comment on why this is the case. I have been able to fix the problem by re-OCR'ing the document, but mostly I just live with the annoyance.
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