Did you get a resolution? Did you send the payroll and did everything go through fine with no duplication issues? I ran an update right before I ran payroll yesterday and now out of the blue it says I have 90 modified paychecks going back to April. I am the only user and did NO modifications, let alone to each and every check for 6 months.  Intuit told me on the phone it is a stuck paycheck situation and to go ahead and send the direct deposit file and no duplications will come up. Looking at the audit trail the only thing I can see is that it would appear the DD check number is missing from the April-Oct checks and then added back in as of yesterday. That would be the modification I'm assuming. I checked the register and my stubs and the register has all of the check numbers listed as they should. Please update with what happened when you processed yours.