Call Chase, explain the problem, and ask them to report the CLs.
I had to do this also. Can you believe I had to explain to the CSR why this was an issue. Then they sent me a letter saying they had reported to the credit bureaus that I was in good standing and had a zero balance. I had to call again, find a manager, explain again. But I also managed to get the annual fee dropped, the APR lowered, and get switched to a better rewards card.