I use Calibre with my Reader. In the beginning I experienced very long pre-pagination times, too. Once it took 30 min (it was a very long book, but still).
Now I don't remember exactly - but I think that after I ran the costumizer hack the second time, it helped. At least it got better after I'd had the reader for some weeks. Sorry I can't give you a better description, but I'm simply not what helped me, but I did have the same issue. Now I don't expect it to take more than 4-5 min. max.
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