This will be due to an issue in your JK &/or SS Payroll Item setup/config.
Check both of these Items & ensure neither are generating the other (ie ticked) on the Inclusions” screen:
Shaz Hughes Dip(Fin) ACQ NSW, MICB
Reckon Accredited Professional Partner Bookkeeper / Registered BAS Agent (No: 92314 015)
Accounted 4 Bookkeeping Services
0422 886 003
As suggested, I have checked both the SS and my JK setups and super is not selected for the JK inclusions nor is JK selected under SS so I seem to have the items correct as per your screenshots.
It is strange that payruns that I have done since are adding SS correctly for that payrun but I am still out because of the offending payrun with the issue. The payrun that seems to be the issue is a payrun that I submitted again as a replacement because I removed the JK Start-FN01 from it as I had this on the wrong payrun.
When I try to reload the offending payrun it still comes through incorrectly even though it is correct in Reckon :(
Really not sure what else to do with this.
I wrote about an issue that I had before about the salary sacrifice and super being correct in Reckon but not in ATO.
I subsequently found a question about a similar issue in this community forum and used the reply from that and so far my issue has been resolved and all my totals are the same in Reckon and ATO. I'm not an expert so I dont know if this will be OK for you too but might be worth a try?
The question that I found (you could search for it?) was "Why doesn't the RESC amount in Payment Summary match the RESC amount on payroll summary report"
The answer was to refresh the specific pay that had the issue.
1.Click on Reports, Employees and Payroll and select Super report by fund
2.Click on modify report and in columns box scroll down to RESC amount and make sure it is ticked.
3.Scroll to relevant Fund and employee to identify which pay should have RESC amount but does not (or any other irregularity).
4.Double click the pay and unlock it
5.Delete the super items contributing to RESC and re-enter for same amount.
6.Repeat for any funds or employees with issues
7.Generate Super report by Fund and RESC amount should now show.
I hope it works for you too.