There are possible reasons why those checks won't show up in your check register. I'll give some scenarios and solutions on how you can fix this.
One probable reason is that your check register is filtered to show selected transactions. You'll want to change the filter options in the account history.
Here's how:
Go to Accounting, then click the Chart of Accounts tab.
Find and select the check register by clicking the View register link.
Click the Funnel icon, then change or review the filters.
You can also check the DATE or Ref No. Type column to sort the transactions.
Another reason is that those transactions might've been recorded under a different account. In this case, go to the Paycheck list and view the paycheck detail. Look at the Paid from section to see where the funds were taken out from.
Go to Payroll or Workers, then click the Employees tab.