@NegevRain - thanks for the link, I downloaded and it worked perfectly for me...
Code:
Starting job: Extract ISBN for 1 books
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Title: Coach Wooden's Pyramid of Success
Format: EPUB
Path: D:\Dev\CalibreDev\TestLibrary\John Wooden\Coach Wooden's Pyramid of Success (878)\Coach Wooden's Pyramid of Succe - John Wooden.epub
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Scanning first 10, then last 5, then remaining 29 files
Invalid ISBN match: 2004
Invalid ISBN match: 49516-6287
Valid ISBN13: 9781441226181
Scan time: 0.72 secs
The isbn was found in 0.72 secs
New ISBN extracted of: 9781441226181
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Scan complete, with 0 failures
This is with calibre 7.7 (yes I have finally upgraded personally from 6.x). You don't say which version of calibre you are using?