Comment 3 for bug 310711

I hope this is ok, but I'm reporting on this to let you know that it's not an Ubuntu-specific problem. I use Fedora 12 and have the same issue.

It doesn't matter how I launch my alltray-controlled apps. Here is how to reproduce:

alltray 0.70
compiz 0.8.2
compiz-fusion 0.8.2
x86_64 architecture

1. Launch any app using alltray with a command such as:
  alltray -s -nm gnome-calculator
  alltray -nm gnome-calculator
  alltray gnome-calculator

2. If the window wasn't automatically hidden upon launch (through -nm flag), minimize it to the tray.

3. Restore it through the tray.

4. Invoke the compiz shade effect (mouse to upper-right corner)

A note -- when you use the -nm flag, these windows WILL appear in the compiz shade picker UNTIL the first time they have been minimized to the tray.