Why wonder?
I just checked my pristine copy, and the italics problems are definitely present there too. The first flashback chapter is all italic. The second one is all non-italic. The third one starts out italic, and shifts to non-italic halfway through the first paragraph.
The scene breaks are simply inserted line breaks like this: <div> <br/></div> instead of having the padding properly defined in the corresponding css class. So that's why they were too big.
The inconsistent gaps under chapter headings are indeed not present in the pristine file, so I will give you that one. That seems to be a weird artifact of Calibre, but it is strange that I haven't seen it in any other books.