I am also having this issue and have called support.  I have not received a ticket number and the issue is not resolved.  They are not showing up in any chart of account.  However they do show up in my payroll report.  One check came through fine on the same day and matched how it should.  I have never had success in calling the help line.  They go through many steps that I had already done then supposedly create a ticket. I have not heard anything back since I talked to them the first of March.