Back when I had an accountant, she entered very different numbers on lines 3 ("wages, tips and othe compensation") and 5a ("taxable social security wages") of the federal 941 form, with a lower number for line 3. The books for my sole member S corp are very simple; there's a 401(k), that's pretty much it. Could the difference be due to the employer (or employee) contribution to the 401(k)? Why would she have entered these numbers differently?
Closely related: are the employer or employee contributions to a 401(k) subject to social security and Medicare? Has this changed between 2013 and 2015?