SEP contributions should be calculated using Net Earnings from Self-Employment, which is box 14-A of Schedule K-1 (1065). Box 14-C is Gross Nonfarm Income, which to the best of my knowledge is only used calculate the optional nonfarm method of calculating self-employment tax. The Business program should be using the amount in Box 14-A. Have you reviewed the SEP/IRA Worksheets in Forms view? Right click on Box 1a. In the pop-up window, click on "Data Source". This shows that the source for "Net earnings in self-employment.." comes from Box 14, Code A, not Code C. The calculation in both programs should be the same.
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