I do not know what the contents of the Goty cd look like. For the retail version if you browse trough the cd you can find the installer in the setup folder. Even if the game is installed, the installer will just install it again. If that is not the case for the Goty edition then we must do some cleaning:
Go to start > run > type in regedit > ok
Open HKEY_LOCAL_MACHINE\SOFTWARE\Activision\ and delete the Return to castle Wolfenstein Goty key.
Next go to C:\Windows and delete the goty.ini file. Not sure if it is called that, I do not have the Goty version unfortunately. I know for the other editions its rtcw.ini and Rtcwplat.INI. If you sort the folder to details and type you should be able to find the ini file that is for the Goty edition.
When that is done try installing again. It should work then.
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RtCW Problems, Errors and Help 
Installation probs. 
Linear Mode
