I have had this issue for as lon as I can remember and have just accepted as the way things are, but today I thought I would tap the collective and see if some knowledge shakes out. I have always been able to see all the folders in my email program ( I use windows live, but I used the built in pocket client in the past with the same issue). If I open the list, all email folders are there, but if I click on one it shows up empty. I use hotmail by the way as my email box. I currently have leave anything I want mobile access to in my inbox - veryannoying.

how are you connecting? do you use imap or pop (also, isnt there a third option to connect to hotmail)?

the way i configured my phone (gmail with imap or is it the special windows live connection for hotmail?) is by opening the account while its not synchronizing and selecting Menu --> Tools --> Manage Folders and checking off the folders you want to synchronize. This only works under IMAP and Exchange.