If coolant isn't been changed in a loooong time (several years), it becomes corrosive. Every passage in the cooling system starts breaking down.
Best for a cure is a continual flushing until the water coming out stays clean...this continual/constant flushing process may take half an hour or more to flush out ALL of the loose particles. You can use a
kit from your local auto supply store, and a garden hose. Be sure to run your interior heater while you're flushing. After that, replace with the proper mixture of coolant and
distilled water. If you're going to roadrace, also add some
water wetter.
Worst case, some of your cooling system's components have become internally corroded to the point of failure, and they will need to be replaced. Don't worry - you'll know when they fail...just keep a close eye on the coolant temp gauge on the dash. Cooling system parts prone to failure in this situation (in the TT - the only model I work on) are the water pump and the pipe that joins the heater hose above the #6 spark plug.
Oh, and get rid of that silly filter the dealer put in ... it'll only impair the effectiveness of your cooling system. I really wish there was a law against dealers' mechanics doing absolutely idiotic 'repairs'.
More info here:
MKIV.COM