Did you have to restore your data from a backup? If so, then any checks created/posted since that backup was made will not be in the system.

If a check was posted, in will no longer appear in the Open Batches screen, but will in both the Check Reconciliation listing and the Audit Trail. Print both of these reports to determine if the missing checks appear here.

Do you have more than one bank defined? It is possible to use the same check number for a different bank code. From the Edit Banks section, a field determines the 'Next Check number' if the checks are printed.

When checks are entered, if you do not have the Print Check box selected, then the check number must be entered manually. Should all of the above not turn up your missing checks, then you can enter a batch of non-printing checks (to match any checks that have already been printed), as long as you are not using check numbers that have been used for the same bank.

From your message, the check numbers have been used. Quik Check for Windows does protect against using duplicate check numbers.