Installing Applications with Terminal Services running.
To ensure that all your Terminal Server system’s users have access to applications on the system, you need to use a certain method to install the applications. Terminal Server has two modes: Execute and Install. By default, all users log on in Execute mode, which lets them run programs. As the administrator, you need to set Terminal Server to Install mode when you want to install an application that all users can access. If you use the Add/Remote Programs Control Panel applet to install an application, Terminal Server automatically sets the mode to Install during the installation and resets the mode to Execute after the installation.
That does not always work for some programs and also for some configurations of machines I have tested the manually way with four different machine/software configurations and it has worked every time. You do need to set it back to execute mode after any installs BUT 95% of program installs tells you to reboot and so when you log back in it is already in execute mode.
To manually change to Install mode, just type:
c:> change user /install
To return to Execute mode after the installation, type
c:> change user /execute
To check your system’s current mode, type
c:> change user /query