Still not clear. Are you using the Windows Home & Business version for personal returns with Schedule C OR the separate Windows Business program? I don't think the Business program does schedule C.
Are you married? Yes make sure all the W2s and sch C are assigned to the right spouse.
Are you sure Schedule SE (for the tax on schedule C) is adding in the full social security tax? You still pay SE tax on the Medicare part. If you also have W2 income, you have to break out the Social Security and Medicare taxes. Only the Social Security part maxes out.
The SE tax includes what you already paid in from your W2 so your schedule SE tax will only be the difference up to the max amount of $10,453.20 for social security. The max for social security for 2024 is 6.2% of wages plus schedule C net profit up to $168,600. Medicare is 2.9% (both er & ee parts) of all wages & schedule C profit - no max.
