Not all the vouchers are printing on the stub and I'm getting the Microsoft Great Plains separate remittance report.

Mekorma reporst when used in conjunction with the GP Separate Remittance report behaves unexpectedly and not all invoices will print on the Primary Check Stub.

Mekorma does have Overflow functionality and this would be recommended for continuation stubs.

The Separate Remittance checkbox on the Print MICR Payables Checks window is checked, or on the Mekorma MICR Setup Window it is checked for pre-printed check stock. If this box is checked not all vouchers will print on the stub and the Microsoft Great Plains Separate Remittance report window will display at the end of the check run. This box should NOT be marked when printing Mekorma MICR checks unless using pre-printed check stock with a single printer that only has one tray.

The Use Separate Remittance for Overflow box on the MICR Setup window is marked. This box should NOT be marked when printing Mekorma MICR checks unless using pre-printed check stock with a single printer that only has one tray.

There is a $0 check in the batch. There is a known problem with some builds of MICR that causes the Separate Remittance checkbox on the Print MICR Payables Checks window to become automatically marked after the Password window closes if there is a $0 check in the batch. The suggested work-around is to print the Check Edit list before printing the checks.
Remove any $0 checks and print them in their own batch. This is fixed in V9.0 for PMEFT. It was fixed by the new PM EFT feature to print $0 checks which prevents the automatic checking of the Separate remittance checkbox. If there is a $0 check in the batch that is not an EFT, the Separate remittance checkbox will automatically be checked. This is correct behavior since Mekorma MICR does not print a $0 check for non-EFT transactions.