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This is a guess: While the book is converted it requres a lot of memory. For a large book it might even mean that the memory in the computer isn't big enough. Then the computer starts using virtual memory which is very slow.
64 bit calibre on a 64 bit OS with plenty of RAM should help a lot.
You can run a system monitor tool in your OS to see if this guess is correct. Check memory usage and usage of virtual memory/swap file while calibre is working.
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