Transactions with a Current Balance of 0.00 will not be selected on the pre-check register. Did you post the batch after printing the cheque?
When printing the pre-check register report, this re-generates the work file that lists all of the invoices and other transactions selected to be paid. From the Print/Post Checks and Advices function, go to the 2nd screen (Payments) and look for a transaction in the grid that you thought should not have been selected. Is there a current amount < > 0 indicated there? If so then it was selected correctly and you didn't create the required batch entry in order to clear it.
Also note that only 0.00 Vendors are suppressed on the pre-check register report with the new option 'Exclude zero dollar amounts', not 0.00 transactions (which should already be suppressed).
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Softrak Tech Support