I was facing the same issue. I contacted the agent I had used for transfer of ownership and he informed me that Capital Value tax on my car is pending and that is why system is not allowing payment of tax until Capital Value tax is paid.
I am not sure whether he is giving correct reason, I thought this tax is paid when you purchase brand new car not for used car. Anyway, I have asked him pay the Capital Value tax and solve the issue of annual tax payment.