I've tried different formatting options in Calibre, but epubs with lots of chapter breaks still take a few minutes to load compared to a few seconds for most other books. I've also had issues with the JBL being able to open eReader format docs at all with lots of chapter breaks. I had the Complete Sherlock Holmes as an eReader DRM file and had to convert it to epub to use it on the JBL. The eReader version gave an error when trying to open and I've ran into that with a couple of other eReader format files.
The JBL opens most of my books, but I do run into the odd problem now and then.
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