Hi,
I have been using Ubuntu 12.04 LTS with Gnome 3.4.1. This problem might have occurred in most of the people. I have setup my Skype to run on startup on my Ubuntu. Most people might have also done that. I don’t know how to add any program to start up so, I logout my Ubuntu and switch to Ubuntu classic and add a new program at startup from the Startup menu. This was the most efficient startup adding without any command line. But while I added Skype on my start up, it didn’t used to show any icon on the status bar nor in any location.
Previously without startup, it used to show up the skype icon on the bottom and could control all the functions from the menu provided by skype. So, I used cairo-dock so that it would help me bringing skype on one click. But, I didn’t want the cairo dock thing and want to make some clean Ubuntu. But the problem was couldn’t get the skype icon. Then I did some research and found that if the gnome-shell is loaded first and the skype was started later, that should do the trick.

So, previously I added to the startup:

And Now I changed to:

And that did the whole trick. The above command runs my skype after 5 seconds. So with some calculation, my gnome-shell loads after 2-3 seconds on startup. So, that might be good set the “5s” to your desired second as per your Linux load time.Enjoy