This shouldn't be a mod issue and I don't think there is any issue with the files.
Unless mods in steam somehow is added to another directory and these files are checked instead. But that doesn't explain why it worked before when someone, in that case, had a mod and someone else didn't have that mod.
So something with the last update has created an issue for some people. You could try to turn off the check-sum check for the time being. But then people can cheat.