Why clearTimeout with millisec argument is not working?

Because you're using clearTimeout() incorrectly. Your code needs to resemble the following:

var x = setTimeout("doStuff();", tempo);
clearTimeout(x);

You are currently using tempo as the timeout handle, which is why it isn't working.

Use the return from setTimeout to pass it to the clearTimeout function :

var timeoutId = setTimeout(callBack, 1000);
//then, later in the code
clearTimeout(timeoutId);

To use clearTimeout you need to pass it the value returned from a call to setTimeout.

var timeout;
// ...
timeout = setTimeout('rotate('+i+', '+base+');', tempo);
// ...
clearTimeout(timeout);

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