We've had the same issue multiple times. One or two checks from each payroll will be visible on paycheck list and payroll reports, but does not show in register and the balance is off because of it. Have called customer service and they just have us delete and rerun the check over and over again until it eventually fixes itself. Clearly a known issue, just like labor showing as unspecified on P&L by Job instead of assigned to the jobs it was entered under on the the time cards. Extremely disappointed both issues have not yet been resolved after months of them knowing about it. QBO seems full of bugs and data disconnections that make no logical sense.