I have had this issue as well from the time unity came out and have
found nothing specifically say how to work around the issue, just "you
need a custom .desktop file located in ~/.local/share/applications/ or
/usr/share/applications".

A bit of research on .desktop files and a bit of comparing existing
.desktop files I found that adding the lines...

StartupNotify=false
StartupWMClass=rdesktop

It appears as if the StartupNotify flags are not sent in the rdesktop
program so Unity can not properly handle icon assignment and mapping the
running program to the Unity launcher.  Using StartupWMClass=rdesktop in
the .desktop launcher tells unity to expect a window with the given
string as its WM class or WM name hint this allows Unity to handle the
as expected.

I have my custom launcher located in ~/.local/share/applications/ for
simplicity and it works fine when dragged to unity.

I also had the same issue with VirtualBox as well but the same work
around allowed it to work as expected.


For those that want more information you can look here
http://standards.freedesktop.org/startup-notification-spec/startup-notification-0.1.txt

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https://bugs.launchpad.net/bugs/746343

Title:
  rdesktop window gets a -?- icon in natty launcher

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