Are you sure that everything is fine?
I just noticed one thing in Sigil, it looks like it's a layout problem or I do not know how to call it :
When the text is condensed, spaces appear :
http://i.imgur.com/C76Fll1.png
But if the text is more spread out, they disappear :
http://i.imgur.com/b6IypzV.png
Moreover, I forgot to mention it, the publisher offers several versions : an epub edition in two large parts and a kobo edition (in epub, that I convert un kepub) in three smaller files. The issues appears only in the kobo version (the part 2/3), so I don't think it's intentional from the publisher. I wanted to get around the problem using the epub version but I can't convert it, the file is too big.