If you have trouble accessing your decks and collections on Dropbox, it's because the app is now restricted to the /Apps/Decked Builder folder as per Dropbox requirements. Just move your decks over to that folder and you should be good to go.
Dropbox is our preferred method of synchronizing decks and collections now as it's easier to work with and is cross platform as well (it's not just limited to iOS).
Edit: as for why we are changing the way we handle Dropbox, it's because we are moving to the new Dropbox Sync API. You can find out more here:
Like iCloud, Dropbox Sync lets you work with your files seamlessly whether you are online or offline, and have them automatically synced among your various devices. Also, our experience with iCloud is that it's proving to be a difficult technology to support and get right.
Edit 2: Dropbox Sync also lets you work with Dropbox files the same way as local or iCloud files. All changes to the deck or collection are automatically saved -- no need to manually load/save decks anymore.
- Tan Thor Jen