I found this problem too on my PRS-350, especially in scientific multi-column pdfs. Examples can be found here: http://www.ncbi.nlm.nih.gov/pmc/arti...f/pq010056.pdf
What I think is strange is that in the Sony Reader Library Software this problem also occurs. Double-clicking a word marks a whole sentence or at least several words. This can also be found on the reader itself.
More common PDF viewers like PDF-Xchange viewer or Acrobat reader contrary are able to detect the end of a word and to mark one word after a double-click, so the pdf structure seems not to be too strange.
This problem is really a bit annoying as I really like the dictionary feature for scientific texts but because of the marking-problem it gets a bit time-consuming to look up just one word as you have to delete most of the input field... But I must admit I'm afraid there will be no solution for this problem...