Employee 001 and 002 are monthly paid employees, they both recieve a Regular Salary, yet every cycle you have to enter a T(Timesheet)..Reg(regular Earnings)...Amt, line for these employees. The other monthly paid employees are processed automatically, without any problems.

Solution:

Employee 001 and 002 are being treated by the application as non salaried employees. Only monthly paid employees are salaried employees, and the 'non-salaried employee' check box in the employees pay profile must be unchecked(Payroll>>Employee>>Employee Pay Profile). By default the non salaried employee checkbox is checked when a new employee is being created from HR.

NOTE: If  you have determined that employee was not processed in a payroll run, you must reverse the payroll before you make any changes to the employees pay profile. After the changes are made, they must be saved(you must ckick on the save icon), this is absolutely necessary for the changes to take effect.