Sounds like your server's screen is bigger than your local screen.
When I connect to a vncserver whose display is larger than my desktop, I can usually scroll around it using the scrollbars in my vncviewer window, but this is a PITA.
I'd solve it like this:
ssh to your server, then give the command
Code:
vncserver :1 -geometry 800x600 -depth 24
Now, back locally start up a vnc viewer:
Code:
vncviewer servername:1
Now the server's window will fit on your desktop, and icons shouldn't "disappear".
Note, in the above, I am using :1 because that is the next spare display I have. YMMV