could you give more description of your IT background.
1. How many forests do you have?
2. Which domain is the user in?
3. Which domain is the linked mailbox in?
4. How do you access to the linked mailbox?
5. Do you create the linked mailbox or convert a mailbox to a linked mailbox?
6. Does the user have the full permission for the linked mailbox?
7. What do you mean by the subfolders? Inbox and etc?
And then, we can research your problem further.
If you want to learn more information about the linked mailbox and how to create a linked mailbox, you can learn from below link:
You can learn how to convert a mailbox to a linked mailbox from below link:http://technet.microsoft.com/en-us/library/bb201694.aspx .
Per my experience, if you set the linked mailbox according to the link, you'll be successfully access the linked mailbox and can see the sub-folders.