1) The Payroll Summary report you mention that's in the More Payroll Reports in Excel using Payroll by Department/Class is helpful, thank you, but where are the hours that show up in the regular Payroll Summary report? We need to tie out those hours by each location and previously the hours were there. Now this alternate report only shows the pay amounts and not the associated hours. 

Has anyone found another report that includes hours??

2) Here's what I found in using the regular Payroll Summary report from the Reports menu/Employees & Payroll/Payroll Summary: when first choosing this report it seems to default to "Show Columns: Employee" where the employee's Taxes Withheld and Deductions from Net Pay (which is actually mislabeled since they are listed BEFORE Net Pay) show and are deducted to arrive at that employee's Net Pay, a Net Pay that is different from Total Gross Pay and Adjusted Gross Pay. But staying in that report and ONLY changing to "Show Columns: Class" makes those categories disappear and allows Net Pay to incorrectly match Adjusted Gross Pay. 

And now, here's what changed: We were previously using in Preferences for Payroll & Employees on the Company Preferences tab the option of "Job Costing, Class and Item tracking for paycheck expenses" with "Assign one class per Entire paycheck" BUT then we recently changed that preference to "Assign one class per Earnings item". Somewhere in that switchover the Taxes Withheld and Deductions from Net Pay disappear from the Payroll Summary report. The Payroll Summary reports for previous payrolls are fine, reports run for payrolls after the switch are NOT! (The only reason we did the switch is that QBks no longer allows us to have more than one active "employee" with the same social security number so we can't assign the separate hours for a multi-location employee on separate paychecks anymore.)