Folders' content doesn't refresh automatically
This can happen if inotify subsystem ran out of the handles. Running python -mpyinotify /path/to/folder should display the requests to the filesystem that all applications can see. In case this does not work, neither will other applications.
The most likely case for running out of inotify handles is that some application (e.g. Dropbox or Ubuntu One) is tracking the changes in the directories.
In this case you will need to increase the value of fs.inotify.max_user_watches sysctl parameter.