Hello and good afternoon, I'm sorry to hear you're having these issues. I believe the mail index in these folders is likely corrupt. Not to worry though, we can get that resolved pretty easily in most cases. Can you give this a shot?
1. Stop the SmarterMail system service.
2. Navigate into each of the affected folders and delete the mailbox.cfg file found there. Repeat these steps in every folder that won't currently load.
3. Start the SmarterMail system service.
4. Clear your browser cache/cookies and log in to the mailbox again to confirm whether or not the issue has been resolved.
If that doesn't help you may need to get a support ticket submitted so we can take a closer look at this. Additionally, as Rose pointed out above it is typically recommended you keep folders at the root, rather than beneath the Inbox directory. Inbox nesting can cause synchronization issues on mobile devices and a variety of other strange behaviors in some cases. Moving those would involve a process very similar to the one above, but we can advise you on that if the steps above don't do the trick. Let us know how you make out :)
Kyle Kerst
System/Network Administrator
SmarterTools Inc.
(877) 357-6278
www.smartertools.com