The simple answer, for the alignment at least, is that you have it set to left align on the device.
Other than that, Kobo uses the Adobe RMSDK for epubs. This is a lot less tolerant for errors than most other applications that handle ebooks. If there is an error in the stylesheet, it can ignore the complete stylesheet. You could try the book with ADE and see what happens as that will be roughly the same as the RMSDK.
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