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Problems highlighting in merged files

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When I highlight one document in a merged set of PDFs (e.g., the article and its supplementary material), the same highlighting appears on all documents. How do I prevent that from happening? Note that this is a new problem in the last month or so. I wasn't having this problem in the past (I use Mac OS X 10.8.4 and Mendeley desktop version 1.9.2). Thanks.

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