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Some things to try:
1. See if you can highlight the text in the viewer.
2. Try to convert into some other format, for example epub (and you can unzip that if you want to check the code, or compare with other epubs to check for odd files)
3. If you unzip the epub, try to open one of the html-s with the browser.
Though the fact that only Calibre viewer balks at the text makes me doubt that #1 gives any results.
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