Josh is out today, but I believe we applied this "auto-subscibe" fix to both shared folders and regular folders across the board. So it should fix both for you. If you still notice folders disappearing/not showing up update this thread and can check it out more.
EDIT: Existing folder properties/accounts connecting to IMAP may retain the non-subscribed setting for their folders. This may mean you need to resync. If this is a major issue we may be able to somehow auto-subscribe already un-subscribed folders.
Matt Petty
Senior Software Developer
SmarterTools Inc.
www.smartertools.com