Kidney stone, CT shows no stone.

I have kidney stone which got detected in May 18 of size 3mm through sonography. Then dr prescribed me to take lot of water. I did sonography after 2 months but stone was still there with same size. This time with water i took some ayurvedic treatment from local and decided to do sonography after 2 months. But after one and half month it started paining in my left kidney. I did sonography immediately August 18. Now i got another stone of 4mm in left kidney. I consulted urologist and he suggested to do plain ct scan and creatinine test. My creatinine is in range 1.00 but ct scan result shows there is no stone and everything is normal. But i am having pain in my lower back, sometime left side, right side. and it's consistent from past few days. kindly help me to diagnose this and to get proper treatment.