I think the retirement contributions is a separate question on the FAFSA, not part of the IRS retrieval (since they don't appear on your tax return). There is a special automatic EFC = 0 if you meet certain conditions, and it kicks in before the add back, maybe you qualified for that.
Google "EFC formulas 2016-17" to get the actual way the EFC is calculated, and the rules for auto EFC = 0, and the simplified needs test. That last one lets you skip entering assets (like your inheritance) that would normally increase your EFC.
Great work on getting EFC =0! I have DH fully fund tha HSA, and put enough in his 401k to get the EFC as low as possible (0 this year), and the most EITC we can manage (not max) while having enough take home. I'm trying to project out for all the years for the kids - it fluctuates depending on how many are in college, how many count as dependents for FAFSA (IRS is completely different), their ages and incomes, etc. More students is not better for us - it drops the income protection amount for the same size family.