Here is the solution:
When you process your payroll and create your Direct Deposits are they marked to be printed? If so, they are probably all sitting in your to be printed file and it’s full. If this is the case you can go to File>Print>Paychecks and send them all to a PDF printer or just to a file on your computer and then delete them from the file later. This will clear out your to be printed file. You can also go to your check register and edit each check removing the To be printed check mark. This would be fairly time consuming though.