Why can't I use the Dropbox Apps folder?
We have had a number of reports where users who select the Dropbox/Apps/ folder for syncing have experienced odd behaviour (e.g. preferences not saving correctly). We believe this is due to this folder being reserved for applications using the Dropbox API (which Alfred doesn't use) and have not been able to resolve this with the help of the Dropbox team.
As a result, we have excluded the Apps folder from the available syncing locations and do not recommend that you choose it as your sync folder.
You can select or create any other folder for your Alfred settings within your Dropbox folder.
What if I want to use that folder anyway?
If you really want to use the Dropbox/Apps/ folder regardless, do so at your own risk. We recommend that you back up your preferences first, as you are more likely to experience issues with saving your preferences. To do this, quit Alfred then open a terminal and run:
defaults write com.runningwithcrayons.Alfred-Preferences dropbox.allowappsfolder -bool TRUE
If you experience any issues, switch back to a sync location outside of Dropbox's Apps folder.