Same problem here! Every time I try to remove a plaque, or pick some items up (such as the medalions), the game would freeeze.
And just like you if I replace the exe file with the original one the game works perfectly in those "black spots".
Yesterday i realized that if in the fixed exe I set the language in Japanese, the game won't freeze but crashes.... absolutely odd.
I have no solution, but well, at least you know you're not the only one. Besides the weirdest thing is that I know of many people for whom the patch works great...
By the way, I'm using the patch just because the trainer won't work with the original exe, is that your case too?
May someone have a solution for us!