After migrating to the new Dropbox architecture and subsequent preferences location change (even thought this worked until yesterday), I got permissions errors about Alfred not being able to write to plist files, even thought the perms were correct.
I worked around it (don't have an explanation as to why this worked) by just moving the prefs folder locally, pointing to the new location and saving, and then copy pasting back the entire prefs folder to dropbox, repointing and now it sees no errors.
Likely explanation: combo of OSX special file locks/checks