With davidfor's information, I figure out what is happening with the book covers.
In 2.4 anytime when you turn off/on the device all the books that are stored on the SD Card will have their book covers regenerated over again. This of course slows down the reader.
With 2.5 all the book covers are saved on the SD Card. This means the book covers are not regenerated every time when you turn off/on the device. This is leading to fast loading of the book covers.
Specifically all the covers are saved in the koboExtStorage\images directory.
I am taking the guess that the current version of calibre isn't delete the data in the koboExtStorage\images which leads to mixed up book covers.
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