@CaptainMorgan: Easy solution for your problem: Never load a savegame created with an older patch version. Taking care for backward-compatibility would hinder my progress and isn't really necessary, since it is reasonable for everyone to patch only before a new career.
Regarding 4GB Patch: Was the CTD reproducable? Or did it occur only once? I ask, because I made a small test:
1) I applied the 4GB-patch using Stieblers Options Selector. Saved the patched file as sh3a.exe.
2) I applied the 4GB-patch using the NTCore from your post. Saved the patched file as sh3b.exe.
Compared both files using
> fc /b sh3a.exe sh3b.exe
Result: Both files were exactly the same. No difference. Everyone can reproduce this test.
Your post above suggests that Stieblers Options Selector does something wrong. The little test above proved that this cannot be applicable.
So there must be a different reason for the CTD.
If one does a certain action called ABC, and after that a CTD occurs, one cannot automatically conclude, that action ABC is the cause of the CTD. One can only make an assumption, and this assumption must be proven to be true by an empirical analysis.
I have even heard of people who have CTD on a fresh and completely unmodded sh3 install: See here:
http://www.subsim.com/radioroom/showthread.php?t=187156
h.sie