That's because the remote control is linked to the executable itself, not the shortcut. In order to make it so that green button won't use the animation, you need to edit it's target parameters as well. I don't know whether there's a configuration tool for your remote settings, but if there is you need to make sure the target for that button has the same settings as the shorcut.
I have no idea on how to do that, I think my RC does not have a setting app, it is an MCE "plug and play" RC.
I wonder if it is possible to change something inside ehres.dll
If it canīt be done, I would be happy to disable the audio.
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Media Center\Settings\MCE.PerUserSettings]
"enableStartupAnimation"=dword:00000000
"enableStartupSound"=dword:00000000