I had a very similiar issue with the Touch and was able to resolve it.
I bought about 3 books from the Kobo website prior to getting the Touch and bought 1 book subsequent to that. For some reason, only 2 of the 3 previously purchased books showed up on the Kobo desktop application. I found that if I went to my account on the Kobo website and then to "My Library", the two books that were syncing were in the "I'm reading" subsection whereas the two books that weren't syncing were not in that subsection. All 4 books did show up in the "Purchased" subsection though and I was able to add bookmarks to the first page of the two problem books from there and that kicked them into the "I'm Reading" section. The Kobo desktop was then able to pick them up.
Hope that was clear/helpful.
Coming from the Sony PRS-350, I'm finding the Kobo desktop software a little wonky.
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