PDF conversion on Calibre is not exactly problem free--and Kovid is the first to admit that. So whilst it certainly could be a Kobo issue, it could also be a Calibre one or a combination of the two. Hard to tell at this point.
There are other problems with sideloaded ePUBs on the new Kobo, apparently, so when they work on that, maybe this will also kinda fix itself. One can hope...
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