Any patch before the 1.06 version required you to set some files to read-only, but with it it's the other way around, you have to make sure no files or folders are set to read-only or has any write protection.
Your saves should be OK as long as you have a similar version and hadn't altered any files in your previous game. The save files store a lot of information, and if you made changes in your ini files it will cuse problems.
Since the kill counter is part of the source code, and you haven't installed anything other than the patch and mod files, I can only guess that you started using a different set of soure code files mid-game. There is nothng else that would explain this and the only fix is starting a new game and keep using that set of source code files through the entire game.
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