I am having a similar problem with cpu usage.
I got a Kindle 3, and through various postings found Calibre to be the only real player in the ebook field. I was actually pretty OK with that, as I have heard many favorable things about Calibre. Setup was painless and it immediately recognized my kindle 3. The problem started when I tried to import my relatively large Ebook collection. I am trying to import 5,000 + or - at a time.
While it is importing it pegs the processor .... I mean everything it can get, as well as maxing out the memory. I have a rather extensive collection of books and that was only one folder. The problem being that it took 3 days to import those, and I have 6-7 other folders I would like in the database with similar size and structure.
My system is relatively old but still pretty snappy
AMD Phenom(tm) 9600 Quad-Core Processor
4 Gb DDR2
2.6.35-24-generic #42-Ubuntu SMP x86_64 GNU/Linux
Any words from the wise would be greatly appreciated !