bro, plz get your wiring checked from a reputable electrician. I had also the same problem with my vitz 2000. I got it scanned and the scanner told that there is some issue in the solenoid of the gear ! And my electrician told me that your car's gear is "FARIGH", plz change it. Then I visited peshawar shoba bazar, got the new kabli gear fitted ! Now, its time for a test drive. And WTF man, the same problem persists, no smoothness and nothing ! I got very very angry with the mechanics ! But they asked me to calm down. Then after a hardwork of mechanic & electrician for one whole night, they finally came to know that there is problem in the wiring grips of the gear, and some signals are not going to the gear from ECU. Atlast, after a 20 minutes task of grip changing with kabuli ones, the car is as smooth as before, everything is working fine till now, Masha Allah !