1. What user are you running under when you exec it from xterm? 2. What does the hildon-desktop script run when you click it? Paste that. 3. Can you change the hildon-desktop script to use run-standalone.sh if it doesn't already do that?
[Desktop Entry] Encoding=UTF-8 Version=1.0 Type=Application Terminal=false Name=stockona Exec=/opt/stockona/bin/stockona Icon=stockona X-Window-Icon= X-HildonDesk-ShowInToolbar=true X-Osso-Type=application/x-executable