Calibre Interactive has a few ways to force the rule file settings to take precedence.
One way is to click the "Load" button near the rule file name in the "Rules" tab/window is being viewed.
Another way is to use the pulldown menus for Setup >> Preferences >> Misc, and click the button for "automatically load rules file". You can choose whether or not you want to be prompted to load that file with the "prompt to load" button depending on how you prefer it to work.
Another alternative is to set those options in your runset file. I believe these are the related options for what we're talking about:
CheckForModifiedRules = 1
ShowModifiedRulesPrompt = 0
Will you let me know if it's what you wanted?
Yes, it works. I never really understood the need for the "Load" button. Now I know.
Thanks for the answer.