I can confirm this!

I am running a clean install of Ubuntu 11.04 64bit classic desktop, with
all updates (31.8.2011). After adding a program to the Startup
Applications everything looks good. After the first restart the set
program starts up automatically as expected. But after that the
~/config/autostart folder is empty and on the second restart the set
program does not start up anymore.

In my case ~/.config/autostart folder was already owned by the
username:username and the permissions were: drwx------. I changed the
permissions to Drwxrwxrwx, but no effect.

As a background, I am building a information Kiosk, so the Ubuntu is set
to login automatically and the program I am trying to automatically
launch at the startup is Chromium Browser. The command I'm using in
Startup Applications is: "/usr/bin/chromium-browser --kiosk
http://www.amusa.fi/ruutu/etela-karjala";

WORKAROUND
================
To stop the Startup Application setting from disappearing I used the following 
procedure. This is not a fix, but I am able to live with this workaround:
1. Set the Startup Application normally [in my case chromium-browser]
2. Set the permissions of ~/.config/autostart folder to: dr-xr-xr-x (chmod 555 
autostart)
3. Set the permissions of ~/.config/autostart/chromium-browser.desktop  to : 
-r--r--r-- (chmod 444 filename) [chromium-browser.desktop is the startup 
settings file the application I want to startup]

This workaround seems to work for me. Naturally I'm now unable to add
more Startup Applications...

-Jukka-

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https://bugs.launchpad.net/bugs/523796

Title:
  Startup list does not save changes randomly

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