What you describe has happened occasionally to me as well, sometimes when opening a book and sometimes at specific pages within a book. The problem usually went away when regenerating the EPUB with calibre. I never found out the real cause but calibre does some things to EPUB, including "flattening the CSS".
I have a Sony 350 and I am pretty sure the 650 and the 350 have the same software for reading EPUB, as they came at the same time.
/Jens
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