I also just upgraded, this time to natty, and the same thing happens.
>From the console, I start vnc server with default settings.  This in
turn launches x-window-manager, which was set to metacity.  When I
connect with the desktop viewer, the "d" key is mapped to "show
desktop".  Also, since I am using xfce4, I can't get to the keyboard
shortcuts to change this.

The workaround is to not use metacity, and update the alternatives to
use xfwm4:

$ sudo update-alternatives --config x-window-manager
here are 4 choices for the alternative x-window-manager (providing 
/usr/bin/x-window-manager).

  Selection    Path               Priority   Status
------------------------------------------------------------
* 0            /usr/bin/metacity   60        auto mode
  1            /usr/bin/metacity   60        manual mode
  2            /usr/bin/twm        40        manual mode
  3            /usr/bin/wmaker     50        manual mode
  4            /usr/bin/xfwm4      60        manual mode

Press enter to keep the current choice[*], or type selection number: 4
update-alternatives: using /usr/bin/xfwm4 to provide /usr/bin/x-window-manager 
(x-window-manager) in manual mode.

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https://bugs.launchpad.net/bugs/670167

Title:
  metacity  1:2.28.0-0ubuntu1: 'd' key mapped to "show_desktop"

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