We had the same problem since early April.  For us, the problem was that the license key for the payroll module was not correctly changed over when we changed some kind of service with Untuit.  As the license key was incorrect, it saw all the old direct deposits of payroll had not been completed and wanted to redo them.

It took 3 hours on the phone to figure it out.

I would start by checking your payroll license key is correct - you may have the same issue we had.  Check all the license keys while you are at it for good measure.  Good luck.