That is an interesting set of results. The missing italics is a long term issue. I have no idea why Kobo haven't fixed it.
- What were the margin settings on the device when you did this? There is a bug in the current firmware that if the margin settings are not the minimum, when a book is reopened, it goes to a page or two earlier than when it was closed. I could see this affecting link navigation as well, but I'm not sure. This should be consistent across the fonts, but, there may be something else going on.
- For the page numbers, did you have the page numbers displayed in the margins? What I am wondering is if the navigation was going to the first screen for a page number.