Hi Snaz,
I'm sorry, I don't know the background of the issue, I just had a hunch that it would work if you'd just sideload (drag&drop) a known good epub. Unfortunately, that doesn't mean I know what could cause the % breaking (either in Calibre or just in a badly formatted epub). Maybe you should rephrase the title of your thread into 'what causes % read to break?', someone more knowledgeable may pass by and have a solution.
I can just tell you that I've never had the slightest issue with it, if I'd had one, I might have looked more deeply into it because I can imagine I'd be pissed off
I looked on my reader, and I found one .mobi (only
) - I leafed through it, and I noticed that it, too, seems stuck on 1% read. So let's just say that Kobo's .mobi support is very superficial