Hello Marc. I don't believe there is an upper limit for the number of folders that can be used on IMAP, but I do know that the user may need to manually select those newly added folders under the Subscribed Folders settings to ensure they sync to the client. Beyond that though, its possible there are account content issues preventing a proper sync as well, so I recommend getting a ticket submitted on this so we can take a look.
Kyle Kerst
IT Coordinator
SmarterTools Inc.
www.smartertools.com