@spagans Well, the most straightforward reason would be that somebody is either creating a small extra paycheck, or slightly increasing the pay amount of an existing paycheck, and not paying the resulting extra payroll taxes.
Since it is the same amount each Quarter, I would assume it is an extra paycheck.
I would start by going to the Employees>Payroll Taxes and Liabilities>Create Custom Liability Payments submenu to find which taxes make up the $45.08 in either of the problematic Quarters. Any given constituent tax amount of this $45.08 can be used to track down the problem child. Medicare, Social, or Federal Withholding.
You should then be able to go to the Reports>Custom Reports>Transaction Detail submenu to generate a report.
Set the report dates to the Quarter you are working with and apply an Amount filter for the tax amount you chose (Medicare, Social, or Federal Withholding). This should narrow the report down and show you the paycheck that contains the mystery taxes. Double-click on the listed amount and it will open the paycheck.
