Good day, @Anonymous.
Let me help figure out why your employees' paychecks are off in the social security section.
It's possible that QuickBooks auto corrects the social security based on the tax rate and wage base of the employee. To verify if there are discrepancies, you'll need to compare the paycheck's calculation of wage base x rate to the annual amount in the Payroll Summary report. Since you manually modify the percentage on the paycheck, QuickBooks will automatically add the discrepancy to the next payroll check.
Let me route you to this helpful article for more information about wrong tax information showing on the payroll information: QuickBooks Desktop calculates wages and/or payroll taxes incorrectly.
Taxes should be fine as long as the annual wage base x total amount calculation is correct.
Please let me know if you have other questions about your payroll deductions. I'm here to help however I can.