Yep, can't beat the machine for doing a quick job and not having to get your hands dirty, but I think all you did was replace the coolant?
At least when I change mine (manually, and yes, it takes all afternoon!), I also run some that 'rad cleaner' through the system. Then I drive the rig for an hour or so, and drain that mess.
I was really amazed at how dirty the water was after the cleaner had done it's job. Before I ran the cleaner through, I too had nice clean water draining out of the rad while the engine was running.
Two ways to go. Do it yourself or pay someone. Each gets the job done, one you have to spend some time, the other is to spend some extra cash on.
My rad flush cost me $12 for two gals of coolant. $4 for the cleaner. $6 for the beers I drank while it flushed. Time spent with my TRUCK "Priceless".........