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Thank you for your reply. The discrepancy here seems to be that quickbooks and turbotax treat the income as when the payment was received, not deposited.

 

So it was received in December 2017, but because of other circumstances, I couldn't get a chance to deposit it until Jan 2018. 

 

So their 1099's for 2017 now looking back, was too little, and for 2018, too much, as their 1099 seems to be based on when the funds actually left their account. 

 

As you say it seems more and more like I will need to amend 2017's return as these funds they have in their 2018 1099 were submitted as general income in 2017. Although that still leaves me unsure of how to include it in my current taxes.