The retail version, that was patched by the launcher when I started the game automatically, does indeed work with the GOG trainer.
Perhaps it may be something with those who manually patched to 1.1? Just thought I would throw this in as a possibility. Hope it helps.
Thx to the hard work workers here at Cheat Happens.
I confirm that the retail 1.1 does indeed with the GOG version of the trainer. Thanks guys.