So you are saying that when you go into Agent Settings | Portal Manager | Branding and change TaskBar Icon and deploy the agent it does not change the shortcut Icon? If so this would be a bug.
That particular setting is actually referring to the taskbar icon (in the upper left of the open Portal Manager window) and not the shortcut icon. I am using a custom icon there and it is working OK.
What I need to change is the shortcut icon which is listed on the desktop, start menu or the program menu. That shortcut icon is literally coming from the LANDesk PortalManager.exe itself.
Currently we don't have a way to customize this icon for the new portal manager but we will be adding this functionality shortly. Hopefully by service pack 2 for 9.5.
We have a large number of our machines with black desktop backgrounds due to policy.. since the new icon is all black we cannot see the icon at all. I also looked for a way to change this icons but didn't have any luck. Hope this gets changed soon. It would also be nice to change the logo.gif file in the LDClient\html\images folder in the branding area.