I've just realized that I'm having almost the same problem on the book I'm currently reading. Luckily for me the margins aren't huge to begin with, but all the margin cut does is slightly narrow the margins on the first page of each chapter and slightly increase the text size on the same page. What the heck? It's not a big enough pain to try to fix at this point, but if I run into another book like I had a while back with 2-inch margins I'll have to fight with calibre about it.
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