If the SS wages are maxed out on the 'other' employer, then (a) the S-corporation pays the employer side of FICA and withholds the employee side of FICA, and (b) when the taxpayer files their tax return, the employee side of FICA is refunded.  The employer side is NOT refunded.

As for why the "Intuit Tax Advisor" program doesn't include that, it is because that is only one of many faults of the program and the 'ideas' it give you.  From what I've seen, that program is severely lacking and mostly deals with very basic things or gives half-truths/incomplete information.