A new Fast Publish KB article has been released yesterday regarding using Remote Apps on clients where the default shell (explorer.exe) has been replaced with an alternative shell.
Article ID: 2695453 - Last Review: April 5, 2012 - Revision: 1.0
RemoteApps has a dependency upon explorer.exe
"...You can customize Windows client systems to the point of replacing the default shell (explorer.exe), and using an alternative shell. If you choose to replace explorer.exe, you will be missing essential windows functionality, however it may still be possible that you will still be able to successfully launch a remote desktop connection to another Windows system.
However, if you are trying to launch a ’RemtoeApps’ and run an application from your server on a windows client that does not have explorer.exe running as the system shell, that connection will time out and fail. This is because the RemoteApps connection has dependencies upon explorer.exe, including but not limited to the system tray for notifications, the language bar for switching languages, tabs for multiple tab applications, and icons and icon overlays..."