I"m having similar issues. I tried to use calibre last night to do some conversions and the pages just don't fill the whole screen for me either no matter what settings I change it to. Browsing through the calibre thread here http://www.mobileread.com/forums/sho...t=27783&page=7
it looks like some people are having similar issues with the kindle 2 but not other readers. I would suggest maybe posting the questions there since kovidgoyal who made calibre seems to be answering questions there with regards to the program and modifying the program as needed based on the issues that come up. It might be a settings thing in terms of the output. People with sony readers don't seem to have similar problems.