It the font size is specified in the CSS file then this will override the settings that Kobo uses. This is per the CSS specification itself. Computer stuff seldom does things at random. If you have a file that shows this and no DRM you can unzip it and look at the CSS data yourself to see if this is the case. If a file is translated from Word then Word always hardcodes the font size and if it is not removed from the CSS you will see this.
Dale
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