There is no way to persist (or programmatically set) the IE Developer tools option: "Always Refresh from Server." Turning that option attempts to force IE to avoid the cache for all requests that it makes, and that would have unusual side-effects and not reflect how any user experiences the site.
Are you possibly changing your web site while the test is running, while the recorder is attached, or even between test runs? It is standard procedure that anytime you make a change to your website that you manually clear the browser’s cache before hitting the changed pages. Clearing the browser cache after any modification to the site is a practice that web developers normally follow, as doing so ensures that only the latest version of the site is tested, and it is tested as end-users will actually experience the site.