SeaBookGuy--I'm having the exact same problem with one of my e-books. Margin cut changes the margins on only the first page. All the other pages in the book have very wide margins. I tried converting from ePub to ePub with Calibre and setting the margins to 0 under look and feel (I also tried setting them to 2.0pts). Neither of these options made any difference at all.
Then, I converted the ePub to LRF in Calibre. This fixed the margin problem--but the resulting LRF has about five blank pages between each chapter. I haven't yet tried reconverting the LRF to ePub, but might try that to see if that will fix the margin problem and remove the blank pages created by the LRF conversion.
Unfortunately, I don't know much about the details of ePub file formation, so don't feel comfortable trying to edit them myself.
I'll post if I find a better solution. For this particular book, I may just end up reading the LRF version--it only has 25 or so chapters and I think I'd rather deal with the blank pages than the narrow margins in the ePub file.
dordale
