I'm encountering this behaviour/bug as well. Read my bug report on launchpad:
The problem is that the Show Desktop button (or key combination) acts like a simple toggle. One click: Desktop, second click: unminimize all windows, etc ... even more: odd clicks: Show Desktop. even clicks: show all windows....
So that means if you click on Show Desktop for the first time, it will minimize everything. Then you open some new windows. Clicking on Show Desktop again should normally minimize the newly opened windows, but instead it toggles to unminimize everything, since it's the second click.
Which is not so smart imo. Gnome 2 (Ubuntu 10.10) is smarter in Show Desktop. It detects any newly active window and the Show Desktop toggle resets itself, so that the next time you click it, it will minimize everything again.
If you would like to see this fixed, indicate that the bug affects you on launchpad. :)