I have PS 4.0 Advanced on a Windows 2003 R2 SP2 server.

I cannot get the isolation environment node to appear in the managment console. I have tried re-installing Citrix using the repair function from Add/Remove and made sure that everything was selected. It is the only server in the farm and also functions as the Licence Server

A command window does not recognise AIESETUP.exe, and I do not get the option to publish an application into an isolation environment.

Any help gratefully received.

Have you verified that AIE is enabled on the farm / server?

From page 254 from the Administrators Guide:

To re-enable or disable isolation environments for a farm
1. In the left pane of the Presentation Server Console, select the farm node.
2. From the Actions menu, choose Properties.
3. In the left pane of the farm Properties dialog box, choose Isolation Settings.
4. Use the Enable application isolation check box to enable and disable isolation environments for the farm.