This should be cross-posted to Payroll for NA and Time & Labor - PSFT (MOSC)
Basically, this is dependent on your Earnings and Deductions setup.
On the second tab of the Earnings Code setup, you indicate which earnings codes add to the FICA gross:
On the third tab (Tax Effect) of the Deduction Code setup, you indicate whether or not a deduction code affects the FICA gross:
There are certain deductions you have that are probably before-tax for federal or state but not for FICA.