I had read about this same problem being faced by someone in early 2007 and it was noted as being resolved at that time in one of the forum posts.
However, I am facing it currently and will like to know how to resolve it as it is very critical for me to resolve it (as otherwise Zimbra cannot be used as offline mail client).
I create few new folders at outermost level (I am aware of subfolders not being sync'ed yet) in Zimbra desktop. I then move mails to these folders from Inbox or other folders. Finally, I turn on the sync for these newly created folders and click on send / receive or check mail or sync button whichever one appears. To my horror, I find that the new folders do appear in Yahoo web mail but they do not contain any mail messages. They are empty folders only. I waited for two days in case the sync was slow but that still did not help.
How do I ensure that each and every mail in each and every folder is sync'd back to yahoo web mail corresponding folder ?