I was having this same problem but I found a novel solution to it.
I have a retail box copy of Sins - Trinity.  I reinstalled in on my machine after a while of not playing, and I had to convert my old Impulse account to a Gamestop account.  After doing this, my Gamestop app showed three games installed, regular Sins, Sins Entrenchment, and Sins Diplomacy, as three separate games.  Both Entrenchment and Diplomacy needed an update, but I got the "game is not registered error" as described above.  So I followed the instructions to make a Stardock account and registered my game, which worked.  However when I tried to run the update patch I got the error messaging saying that the game was not installed on my system, same as mentioned above.
 
Now, in the Gamestop app I had a fourth game listed as available for download, Sins TRINITY.  It was a ~2 GB file, so not wanting to download it again I tried something.  I went to the settings menu and clicked on "Detect Application" and chose Sins TRINITY from the long list in the dropdown menu, then browsed to my game folder (just the upper level folder, not the subfolders for Entrenchment/Diplomacy, etc).  After doing this, the Gamestop app recognized my version of Sins TRINITY as being locally installed, I just needed to click "UPDATE" to get the updated version.  I had a few bugs during installation but I quit and restarted the Gamestop App and continued the update successfully.  Afterwards when I tried launching the game I needed to enter my Stardock account info and the game code again, but it worked.  Now when I run the game I see 'Trinity v1.37' in the corner, so it seems to have worked!
Hope this is helpful.