I am also having the same problem with my Cultus in 3rd , 4th and 5th gear -- I will be replacing the whole gear set with 08 modle cultus from shershah next month for Rupees 7K.
Its a gear garrari problem, the car might did some runs on low gear oil, for which the friction inccreased resulting a noise.
I my case was the gear oil bolt was not intact properly while changing the gear on Highway for which my top gears started making noise .... mine is a self purchased car 0 meter in 2006.
The only way to get it solved in replacements with the one which does not makes the noise, no need to spend the money here and there, trying to get it repaired, it will not help.