I have converted 2300+ books to epub and I have had maybe 1% of my books have margins set for the book.

It is interesting how often people seem to run into this. Good directions just click to open in the book details panel then open the epub in Sigil. Just for clarification once you do a epub to epub conversion the file in calibre is over written. Since I'm somewhat computer illiterate this HOWTO would have at least saved ME a ton of time figuring out how to fix this problem when I first had it. I DO wish that Calibre could do this by itself, as it takes like a minute per book conversion, but its not the worst thing in the world. Everytime i've followed this procedure it has worked very nicely. Now when you put the file on the device it should be in a nice normal format. Again make sure under 'Page setup' it has 0 for the left margin value (it should if you did this before). Back in Calibre all I do is click convert to Mobi this time to make a Kindle compatible file format. In the style sheet, all I do is look for every single thing that says marginleft OR marginright and make sure the value is 0 for everything. Go under the folder 'Styles' under the Book Browser, and open the Stylesheet.css

If it doesn't open or has an error it might be the old file you are opening, not the new one. Then go into Sigil and open the new Epub file (it should automatically update or save in a new location). First go to Calibre and convert Epub to Epub (yes the same format), making sure to go to 'Page Setup' and change the left margin to 0. If anyone wanted to know the quick step by step I am doing to solve the problem I'll describe it below.

Calibre epub to mobi