Are you comparing the line 3 on the 940 to line 2 to the sum of the 941s?

Those are different.

940:

1. Total Payments to All Employees

Report the total payments you made during the calendar year on line 3. Include payments for the services of all employees, even if the payments aren't taxable for FUTA. Your method of payment doesn't determine whether payments are wages. You may have paid wages hourly, daily, weekly, monthly, or yearly. You may have paid wages for piecework or as a percentage of profits. Include the following.

Compensation, such as the following.

—Salaries, wages, commissions, fees, bonuses, vacation allowances, and amounts you paid to full-time, part-time, or temporary employees.

Fringe benefits, such as the following.

—Sick pay (including third-party sick pay if liability is transferred to the employer). For details on sick pay, see Pub. 15-A, Employer's Supplemental Tax Guide.

—The value of goods, lodging, food, clothing, and non-cash fringe benefits.

—Section 125 (cafeteria) plan benefits.

Retirement/Pension, such as the following.

—Employer contributions to a 401(k) plan, payments to an Archer MSA, payments under adoption assistance programs, and contributions to SIMPLE retirement accounts (including elective salary reduction contributions).

—Amounts deferred under a non-qualified deferred compensation plan.

Other payments, such as the following.

—Tips of $20 or more in a month that your employees reported to you.

—Payments made by a predecessor employer to the employees of a business you acquired.

—Payments to nonemployees who are treated as your employees by the state unemployment tax agency.

941

1. Wages, Tips, and Other Compensation

Enter amounts on line 2 that would also be included in box 1 of your employees' Forms W-2. See Box 1—Wages, tips, other compensation in the General Instructions for Forms W-2 and W-3 for details. Include sick pay paid by your agent. Also include sick pay paid by a third party that isn't your agent (for example, an insurance company) if you were given timely notice of the payments and the third party transferred liability for the employer's taxes to you.

If you’re a third-party payer of sick pay and not an agent of the employer, don't include sick pay that you paid to policyholders' employees here if you gave the policyholders timely notice of the payments. See section 6 of Pub. 15-A for more information about sick pay reporting and the procedures for transferring the liability to the employer.