HI Manas,
Yeah first check the work schedule rule assigned to the employee whether Saturday and Sunday is Off and then if its non working day and then also the absence days is shown as 2 it means its not considering the Saturday and Sunday as absence days.
So the problem is there with the configuration as i said before check for the table V_T554S and maintain as K - Calendar days for the absence type privilege leave.
Also the other check is check in the table V_554S_Q what is the counting rule assigned to the absence type privilege leave and for that counting rule check in the table T556C see to that whether you have check the Saturday and Sunday - Refer to the screen shot pasted in previous reply.
Regards,
Mithun K