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I have found a solution to my problem.
Basically, the problem was that my XML editor, Oxygen, has a 'pretty print' formatting command which cause windows line breaks to be introduced when XML lines get too long to make things easier to read.
I was saving the files with these line breaks included. Instead I should have been saving the files using the Document>Source>Join and Normalize menu option (Ctrl J). This removes all of the offending line breaks and solves the search problem within the db.
Hope this helps someone out there.