Rather than putting the command itself into the startup list, try writing a script, making it executable, then adding the script to the list of startup applications.
Make a new file in your home folder called .startskype and put the following text into it:
echo username password | skype --pipelogin
Then add that file to the list of start up applications.
chmod +x ~/.startskype
Note: Files beginning with a "." don't show up unless you turn on "show hidden files" in your file manager. Ctrl+H usually toggles this.
Note2: It's been a while since I used GNOME2, and I've never used GNOME3/Unity, so I can't guarantee that this will work for you.