Easy there, Trigger. I took responsibility for making this work with the new engine and even added a couple features, like the ability to move the menu backscene camera to suit your perspective tastes; that was what I signed up for. I had in no intention, nor inclination to support all aspects of this mod beyond that. Still, despite that, I still chipped in and fixed many problems in the original scripts of this mod and helped to complete the Dutchman Quest; this thread is a testament to that. At this point, I assumed ownership of bug fixing for what I see claimed as your particular version of this mod, would be taken up by you.
This error:
RUNTIME ERROR - file: seadogs.c; line: 401
Can't open save file: SAVE\Player\Player QuickSave
Is only due to hitting the F9 key, which is mapped to 'QuickLoad'. However, if you have never hit F6 to create a QuickSave, the file is not there, and you get that error. If you hit F6 first, you will see a QuickSave file get created in your save profile directory, and if you then hit F9, it will load that same file and no error presents.
I have made no changes to the original encounters_map.c file, so if there are runtime errors like you describe, I did not introduce them. But, it is a script issue, not an engine one.
I have also made no changes to how the options file is saved/read. If it is not loading the options the way you expect, it is mostly handled in the script files. However, what you describe is actually common; the same behavior exists in COAS. The options file exists in the root game directory, and for new games, those are the options read in from the file and used. When you create a new profile, those options are copied to an options subdirectory in the named save profile directory. If you change the options on the main menu, it does not change the options used within each profile and you have to load a game from that directory and then change the options. The same problem exists when changing key mappings and other game settings that are stored in object attributes...when you load the game, those options have to be changed, then the game resaved again to store, as most of those types of option settings get written back into the specific save game data because they had been stored in gameinterface object attribute values, and not re-read from the options file. It has unfortunately always been that way.