Question: 

1. Can you please explain how the lump sum tax offset calculated?

2. Why has it not allowed the full amount?  I believe that the client is in the 45% marginal tax rate for sources of income without any offset so I can’t see any reason for reducing the full entitlement?

Answer: 

1. Lump sum tax offset is Tax on taxable income less tax on income rather than Lump sum A less tax on Lump sum A.

The offset is the difference between the marginal rate on the income and 30%

Ref: https://www.ato.gov.au/rates/key-superannuation-rates-and-thresholds/?anchor=Superlumpsumtaxtable 

2. Calculation of Lump sum tax offset is rather complex. If user thinks that something is incorrect he can lodge the return and wait for the NoA (about 1-2 weeks after lodgment) with correct amount.

Also I should notice that different tax rates are applied to parts of income below and above ETP cap - 

https://www.ato.gov.au/rates/key-superannuation-rates-and-thresholds/?anchor=ETPcapforlifebenefitterminationpayments

The refund value in LodgeiT is calculated by an algorithm we build. If the ATO estimate is different, we will need to investigate.