The preference: "My Account -> Preferences -> Banner Preferences -> HTML Banner Options -> Automatically alter HTML banners in order to force click tracking" has no effect.
Previously, this preference was used when creating a new banner to determine if the Alter HTML box was automatically ticked.
Since ticking this box has little (or no) effect unless the corresponding adserver is also set correctly, I would suggest that this preference is no longer relevant.
If the box is ticked, and an adserver is selected, the appropriate changes are (now) made to the banner. (the preference only affects new banners).