I have tried pretty much everything for the last 2 weeks to synchronise my hotmail-folders but have resigned to the fact that it will just not work. So, to get around it, I have opened a GMail (Google Mail) account, this synchronises beautifully not only email folders but also my calendar, contacts etc. Then, on the Mac, where I managed to at least import my Hotmail folders, I have created exactly the same folders I have in Hotmail under my Gmail account. Then copied the content over, folder by folder and here they are, sitting beautifully under my Gmail, same old thing, just different email account! Then I set-up a rule within Hotmail to forward all my hotmail emails to Gmail and then you can set-up within your Mac Mail preferences if you want to reply from GMail or Hotmail, etc. Once I am happy with this I will send out an email to all my contacts that they should start using my Gmail from now on. So, all in all that works ok so far, I am migrating everything over to Gmail but will leave my Hotmail active for the time-being, for the odd email that might still come in from people who don't know my new Gmail yet (but which automatically goes into my new Gmail account, as I have set-up the rules there...)
The tricky thing was moving my Hotmail contacts to Gmail in exactly the same format. That needs fiddeling with the export excel sheet, otherwise you loose some data. But thats another story and there is pleny to help on the web too. All in all, I think that is the best solution to get around the problem.