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Well all of my books are Calibre converted mobi - my entire library. Even the ones that I purchased from Amazon get loaded into calibre and reconverted. The only special settings I use are
set font to 12
set justification to left and then an indent
put a space between each paragraph
My dictionary definitions pop up ... well I've never actually timed it but I'd say within a second or so of the cursor hitting the word.
You say something looks funny with your indexing. I'm not sure how the dictionary itself is indexed or even what dictionary you are using - but maybe that is your problem? The Kindle is having a hard time finding the right word in the dictionary? I'm not sure why your Calibre converted books would be different than your Amazon books in that case though.
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