For anybody coming lately to this issue, I want to just post the solution I got. I just changed my PWM frequency from 5000Hz to 4500Hz and the harmonics problem disappeared magically. So, it must be resonating with career frequency of AC as I feel. I am in India and we use 50Hz AC mains that might got resonated with pwm frequency.
Anyway, just change your pwm frequency and see if it solves your case too!