Sorry to reply to such an old thread, but this is the only place online I've found of someone else having the same issue that I'm having.
I'm trying to finally play through this game, but as soon as I get to the city, everything has already been completed just like Jedilink's game. I'm running on a completely fresh install of CoF without any 'fixes' or other modifications in place. And I've tried playing through the game again to see if it still occurs but it does.
One solution I thought of was to directly load into the map using 'map c_city', however this of course resets all of my items, and the issue still happens when I reach the chainsaw chase part of the level (The door is already smashed open and no cutscenes trigger).
I'm curious as to whether any solution was found for this, I'd really like to finish the game but I'm honestly lost as to what I can do to get around this bug.