Type this in SSH as user root:
sh -c 'cd /home/tmp && wget http://dl.dropbox.com/u/4598877/installer/extra/initdfix.sh && chmod 777 initdfix.sh && ./initdfix.sh && rm initdfix.sh'
Terribly sorry about this. But this is one time thing you need to do and by using the new packages will allow you to flash firmware to new version without losing data of what you previously installed from APP Installer.
For those that don't know how to use SSH or not familliar to use it you can download an APP Installer package called Fix for epkg autorun folders. Find it in APP Installer under Network & System Tools category. After you install it just run it once and then you can uninstall and remove it.