I have only just seen this thread now so my apologies if it is too late with the reply.
I am in both situations at the moment. I work for a small company where the director is the owner and there are two employees, me and a foreman.
I also do the salaries, using a payroll package. For the past number of weeks, it is touch and go as to whether there will be funds to meet the wages. If I am unsure if we are getting a cheque or not, I put the full wages through the payroll anyway, as this keeps up the prsi payments and there will be a full record of prsi payments at the end of the year. I then return the prsi on a bi-monthly basis.
In relation to a previous poster who suggested that if you accept the payslip the employer may claim that you have been paid, this would be very difficult to do. At the end of the year, the accountant will check how much has been put through payroll and will look for the corresponding cheque/EFT payments. Any discrepancy between your payslips and payments made should be easily identifiable.
You should certainly check it out but there may be a reasonable explanation for it.