Well I recently had a similar problem with our new coffeemaker and had to get the manual out. It turns out I didn't actually clean it, I just brewed a few pots of vinegar! You had to actually set the coffeemaker to "clean" vs. "brew" by pushing the button until the "clean" light stayed on (it was flashing like you are saying). Then I ran a few more pots of vinegar through on that setting and the light went off when it was finished.
So I'm not sure if that's your issue or not, but you might want to look at the manual.