It's hard to work out the best solution without being able to look at the book, derfel_spain, but here is a suggestion you could try:
When you click on the "Convert Book" button, and select MOBI output, click on the "Look and Feel" option in the menu on the left of the conversion window.
In the box labelled "Extra CSS", type in the following text:
p,div {margin-left:0;margin-right:0}
Then go ahead with the conversion and see if that fixes the margin.
If it doesn't, try again, but this time in "Extra CSS", try:
p,div,blockquote {margin-left:0}
I'm not too happy about trying this, since it might interfere with formatting in other places in the book that you want to keep, but it might at least help to pin down what is causing the problem.
Another option would be to use the Sigil application to edit a copy of the EPUB, and try to fix the formatting that way, but if you haven't used Sigil before, you might prefer not to try that. There's a Sigil forum here in MobileRead with information about the application and links to download it.
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