I know its not much help to add a "me too" but I have always managed to successfully download calibre onto Ubuntu. For various reasons I did a fresh install of 9.10 and I thought that I was missing dependencies when I couldn't install 0.6.45. So in that sense I was glad to read that others were having problems too.
I've installed 0.6.13 from synaptic. Hopefully it'll get sorted in time
