It is important to run startup wizard setting Kobo Touch as your e-reader. I use Sony t1 reader and kobo readers. If I don't do this before connecting Sony PRS-T1 after using Kobo readers Calibre doesn't work right with the Sony reader. Calibre tells you what kind of reader you have connected but doesn't automatically make necessary changes.
What is the source of your books? KT probably is still more sensitive to some book formatting glitches than other e-readers. Try known good books to see if that works.
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