Once again, this is a timing issue. All that mental anguish could have happened in an instant. Plus, Sasuke's hand was inside the shield (possibly even inside Gaara), so we can't tell if the chidori completely died down. In any case, if Kakashi said it was two times max (safely), and Sasuke was debating whether or not to use it the third time, I think it's safe to say that he used it three times, with the seal on the last.
You get a shot of Sasuke's hand on Gaara's shoulder, where he wounded him. There's clearly no chirping or sparkling Chakra anywhere.