http://getsatisfaction.com/kobo/topi..._will_not_sync
According to the Get Satisfaction thread they have known about this issue for "at least two months" and it affects Android as well. Kobo, please fix this!
I have a ticket in with Kobo that has graduated to tier 3 support, and I provided them with a ton of information to hopefully reproduce the problem. Not holding my breath just yet, though.