If you go into manual processing the check does not show up. We've tried reposting, we've tried running the repair, nothing seems to help.  The fact that they add into running totals would suggest they posted,  but they don't show up anywhere and don't add to the employees YTD earnings, which would suggest that they didn't post...

Support is as confused as us because apparently it "should be impossible for a check to post to one place with out posting to the other too," and yet here we sit.... And there seems to be no rhyme or reason to which checks are missing. 

For accounts that we do monthly financials for we will catch the issue every time we reconcile their account at the end of the month. The issue is going to be clients that we do payroll only for since we're going to have to go back and review all the payrolls before we print w-2s to make sure that they are correct before printing.