Hi Shilpa,
Sorry to reply you little bit late. Yes there are so many Payroll softwares been available in the market. Mainly based on Visual Basic, Foxpro, MS Access etc..
Shilpa to cope up with these kind of problems you just prepare an amendment in the existing HR policy, those who will come late after the 15 minutes of scheduled time, after doing so for more than 3 days there will be Leave without pay for half day or you can say salary of half day will be deducted.
I hope it would be more effective after coming into practice.
And regarding warning letter you have a talk with him and make him clear that these are the penalty which we are going to implement, so change your schedules. And try to know the exact reason behind that, because we are not in the system to make it more complex we are in the system to run it more smooth.
Regards,
Amit Seth.