Same issue on Wily.
Adding StartupWMClass to .desktop file works around this issue:
$ cat /usr/share/applications/byobu.desktop
[Desktop Entry]
Name=Byobu Terminal
Comment=Advanced Command Line and Text Window Manager
Icon=byobu
Exec=env TERM=xterm-256color byobu
Type=Application
Terminal=true
Categories=GNOME;GTK;Utility;
X-GNOME-Gettext-Domain=byobu
StartupWMClass=gnome-terminal-server
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https://bugs.launchpad.net/bugs/1503418
Title:
[REGRESSION] launching byobu from unity uses the terminal icon rather
than the application icon
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