My client has a schedule C. The SE Tax Deferral was calculated to be $1,757.

They signed the 8879 April 12, showing a refund of 5,446. 

For whatever reason, we e-filed the return over a month later, May 23. The refund on the e-filed return was 3,689. The difference is the 1,757 se tax deferral. 

Why would this have disappeared? Was there a ProSeries update some time in there which would have changed this deferral? I have not found anything that says the law (and therefore the 1040) changed, that would affect the SE Tax Deferral. 

The client is questioning why their refund was short. 

Has anyone else had this problem?