I suspect they`re not working from your new drive at all. You`ve simply copied them there. When you install a program you normally are asked where to install it and by default this is usually set to c:\Program Files\ - this then registers the location of the .exe in the registry.
To remove the program you need to use Add/Remove programs. trying to manually delete the .exe files will result in the program not running at all and then you probably won`t be able to remove it properly, corrupting the registry.
Why do you want to install programs on your new drive? Why not use it for data e.g. Move your "My Documents" to it. Then if you have any problems with your C drive and need to do a re-install of your OS the data will be intact.