Kobo - pages out of sequence in ePubs

[mamon77]

Hi,
I have a following problem with my Kobo: I have a few polish e-books which were published as pdfs. These pdfs don't look very well on kobo so I used callibre to convert them to ePubs.
Things are great on my Sony PRS-650. But on Kobo, everything is fine at the beginning but in some books once I get to a certain page, a page turn results in Kobo jumping back several pages and there is no way of getting beyond that original problematic page - once I reach it an flip a page it goes back again, and as a result I cannot go through entire book.
Something must be going wrong with the conversion, but I don't even know where to begin debugging it. I tried all kinds of settings and at one point though I had figured it out as for one book the conversion with heuristic processing turned off resulted in a book which I was able to read to the end. But for other books it doesn't help. I though it may have been the ePub splitting setting (default at 260 kb) but I tried various settings but the results usually is even worse.
Anybody experienced anything like that, or knows how to approach this problem? I searched all over and either I'm the only one with this porblem, or I'm not hitting the right keywords as I cannot find anything similar to my problem.
Thanks