This error is indeed annoying. I have to dismiss the message 6 times every time I create a new project. How often you get the message depends on the materials that are applied to your IDs. The standard chrome for example causes 6 popups, Quartz causes 4, Fresh Asphalt causes none. I'm running CS4 11.0.2.
Could also checkout modding resources as well, tons of walk through's posted by the community on this and other specific issues. Modder Base Street Fighter 6 Moddng Tutorial Guide