Yes, I believe it is an amended Form 1040x issue due to the fact the Schedule C Net Profit exceeds SE Social Security (SS) (Fica) wage limit. Then the same taxpayer/sole proprietor has a W-2 from a different business with SS Wages, SS Tax Withheld in the amount of $1,240.00.

The taxpayer is a major shareholder, director, officer and sole employee from a LLC treated as a C-Corp Entity for tax purposes, and also receives revenue on Schedule C as Sole Proprietor of a completely different business services.

Question: 

Am I correct in saying taxpayer paid full FICA Tax on the Original Form 1040, Schedule C Net Profits?

Then once the W-2 FICA Wages and Tax Withholding of $1,240.00 was included on Form 1040X that caused Excess FICA Tax Withholding (an overpayment) from the original filing?

First Issue: When originally filed the Form 1040, Schedule C, without the W-2:   The maximum SS Wage calculation on Schedule SE (Section A -Short Form) = $8,240 ($132,900 x .062 employee share). This amount is included as "Other Taxes" on Form 1040, Schedule 2, Part II, Line 4.   (...Yes the employer share and both sides of Medicare carries to the same line...). The W2's SS (FICA) Tax Withholding of $1,240.00 is not included at this point.

Therefore, the taxpayer has met the Maximum SS (FICA) Wage Tax just on Schedule C net profit. The FICA Wage tax would have been satisfied and paid in full, an extra $1,240.00. In the end, the taxpayer netted a refund on Form 1040 Lines 20 and 21. As of this writing, the taxpayer received their refund;

Second Issue: As the W2 is added into the equation Schedule SE changes using Section B-Long Form. The Long Form = $8,240 [($132,900 - W2 SS wages) x .062 employee share]. In this scenario, the difference between Fica Wage Limit - W2 FICA Wages represents the amount remaining as Schedule C net profit FICA Self Employment to be taxed as FICA Tax. The W2 has FICA Tax Withholding of $1,240.00 so that is being added towards the maximum FiCA Tax of $8,240.00;

Result: There was an overpayment of SS (FICA) Tax of $1,240.00 based on Schedule C Net Profit. Thereby, in my opinion it is reflective as a Form 1040 Excess SS (FICA) Wage Tax to be corrected on Form 1040X.

Problem: During research on IRS Publication about Excess FICA Tax, the writings only addressed having more than one (1)  W2 from two (2) different employers. IRS Publication references if not a 1040 refundable credit then request the refund on Form 843.

ProSeries handles more than 1 W2 from 2 different employers calculation and appears on the appropriate refundable credit line.

In this situation, appears need to override the Form 1040, schedule 2, Part III, Excess Social Security/RRA 1 Tax Smart Worksheet.

In This issue, ProSeries is not calculating the differences yet appears the software is recognizing that it is a wash (not to confuse term with Schedule D Capital Sales of gains/losses) and there is no additional FICA Tax to be refunded;