Hello Shaz,
Yes a common issue with Terminal Services.
There are various methods of limiting the start menu (depending on the version of Windows installed on the server), however these methods will limit yourself also, which means everytime you need to shutdown/reboot a server, you will need to physically go to that server. These settings can be found in both your local policies, but you can also do it through the registry:
Registry Tips (look for "Restricting the Start Menu, Explorer and the Desktop).
Also, I would consider using CITRIX if you have quite a few users. I does cost a little, but it means you have much more control over your users and what they have access to. You can even publish individual applications instead of the entire server desktop.