I'm using Thunderbird 24. If I show folders in Unified mode, my inbox folder shows up twice. If I choose the "All" folders mode, I see only one inbox.
The issue started when I was using Ubuntu 12.04, but now I'm on Fedora 19. (I have migrated the folders on /home). I do remember having it not-duplicated, but then it started while still on Ubuntu.
I noticed it when using the Converation plugin, but I had previously used the plugin without it happening. I have disabled the plugin and it persists.
What I have tried
If I close Thunderbird, rename the .thunderbird folder on my /home to something else, then it will create a new config profile, I have to set up everything again, and then it works as expected, see images below:
Before resetting
Unified vs All Folders
After resetting
Unified vs All Folders
(I'm trying to avoid resetting the profile and creating a fresh new one, because the server -- MS Exchange -- doesn't support IMAP labels, so I'd lose all the tags on my messages, and I have organized it based on tags instead of folder).