Payment stub data does not conform to check amount

we have an issue which is confounding us

We create a check for say 40.25 which corresponds to the invoice amount that we are paying

but the stub amount is including a  -1.00 payment amount with a reference number 0f -1 and totaling this with the stub infomation so the stub amount shows as -1.00

                                                                                                                                                                                                                                                               40.25

                                                                                                                                                                                                                                   TOTAL               39.25

which upsets the vendor and does not look professional--we cannot trouble shot this problem and can not reproduce at will

can anyone suggest why this would happen and where to correlate the stub info to the payables invoices that it is finding