I'm not exactly sure what you are trying to accomplish, but it looks like the clock running while you take images causes problems. The solution would be to stop the clock by taking the battery out, then move it manually to the position that you want it to be in and take the image.
I am trying to capture the clock the moment the seconds hand move across all the hour's (1..2..3..4.. ..12). This make a min. just when the 1 min is over the time is 12.01. where as I want the still time of 12.00 Maybe you are right. I'll have to manually set the time and go on.
I'm afraid I still can't follow your reasoning here or there is a fundamental misunderstanding of how a clock works. A clock measures time. After 1 minute passed, the minute handle will have moved to indicate exactly that. You are asking for a minute handle that stays in place while one minute is passing. There might be clocks that tick this way, but if yours doesn't, you are out of luck.
This would definitely be tedious
I strongly disagree. You want to take 12 images. How is turning the second handle of a clock to 12 positions tedious? This shouldn't take longer than 5 minutes to do.
when I am trying to stack up the photos stacking becomes abnormal
Simply don't stack the images in the area where the minute handle is moving. The minute handle rotates 6° in 1 minute and never reaches an hour mark. Take the one exposure with the desired position of the minute handle and put it on top of the stack and mask it or cut it so that it shows the stack underneath where desirable.