Check your temp files folder and delete the ones related to Vintage Story. When you run the ModMaker.exe program, it stores some files there when first run and then detects those files stored there whenever you again run the program and builds the mod off those files, which look different somehow to the modmaker program than the vanilla files do.
Not sure if that is your problem, but I'd start there if you have not already.
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Thalius's post in ModMaker.exe False Positives was marked as the answer.thumb.png.265fa36120bda8f2d3e72e297b65cfdd.png)