I also have the same problem of patch 1.3 not recognizing my game. My answer to the questions would be:
*What is the version of Ghost Recon -v1.0.0.0.
*Which of the patches are you trying to install? -v1.3
*Did you get your Ghost Recon CD with an MSI graphics card ? -No
*Have you moved GR since you first installed it, maybe to a different drive/partition ? -No
*You are using a retail version of GR from a CD and not some copy, yeah ? -Yes
*You haven't changed the original .exe file for a "modified" one have you ? -No
Thanks in advance