The system uses a consecutive voucher number which gets changed to a check number when the check is actually printed. 
At the time the voucher is created a record gets written to the Accounts Payables vendor history.  If the voucher number matches another history item with the same number, the error message is generated.  Typically the problem occurs when a check number from an old vendor history record matches the current voucher number. 
To get out of the program error message, press Enter to cancel until you are back to the menu.  Launch Tool #639 "Print CU Checks" and delete the vouchers that show duplicate numbers.  Void the checks that printed incorrectly. 
To prevent this message from occurring in the future, an accounts payable purge should be run.  (This feature is located in CU*Answers Operations File Maintenance/Purge menu--online credit unions must contact a Client Service Representative for assistance.)  We recommend keeping just 3 years of vendor history.  Typically, this problem occurs when a credit union has over five years of history.