So it's only two particular folders that has this problem? Are there other folders with as many emails or more in them that work? If not perhaps the number of emails is the problem.
Did you try to create two new folders and try 1) to sync the new folders empty, and 2) to copy the emails in the two trouble folders to the new ones and sync?
I don't know if an upgrade to paid 2Gb Hotmail account will create these problems but then I would think nothing would work and not just a couple of folders.