from my point of view, may be wrong as well 
, please wait for others to reply
1. For one Employee ran the payroll for the year 2015. Whereas from Sep to Nov '2015 around 63 days it was LOP. ------- for which month are you running the payroll 1st?
2. Already payroll run for those period and payment not released.------ what does this mean? you have not paid the EE yet?
3. In this month entered 63 days of LOP for the period of Sep to nov'2015 when we are running payroll for the month of Jan 2016 basic pay showing as negative----. i am not sure why you have to make it as ZERO this is the standard behaviour
4. I want to make the system in the case of full month of LOP it should be zero not to show as Negative. --- 1. as far as i am aware you can make a make a payment for the negative amount then make it as ZERO (if your client wants this) 2. may have to write a PCR to pass the /561 to some other wagetype 3. not sure whether there is a setting in the payslip config in PE51
i am not able to understand why do you want to make it ZERO
for example EE monthly salary is 22000
Jan 2016
basic salary (Jan 16) --- 22000
basic salary (lop)-------- 45000-
Net Pay ------------------- 23000-
Feb 2016 -----
basic salary (Jan 16) ------------------------ 22000
basic salary (lop) by wagetype /561 ------23000-
Net Pay ------------------- 1000-
if you make it ZERO employee will be think that this month he did not get paid due to LOP then next month he will be getting paid. but when he receives next month payslip he will be confused of what is happening how much is the deduction.
regards
rahul