Last payrun of the year missing but was included in EOFY
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Hi @Rav , it’s that time of year again that I turn grey due to issues with Reckon reconciling glitches. I’m needing assistance please. I have already completed my EOFY finalisation for 2024-2025 and submitted it last month. Figures were correct and balanced with my BAS figures…all was good. Unfortunately my accountant has noted on the ATO portal STP a variance in these figures for EOFY 2024-2025. How can this be when the Reckon EOFY figures I submitted were correct? I investigated where the variance could be from and discovered that my last week payroll entry done and paid on Fri 27/6/25 is not included in the ATO STP figure. (Yet it was included in my EOFY finalisation figure as stated above). How do you suggest I proceed and rectify this?
with Thanks, Tania0 -
@TLee where exactly in the ATO Portal is this difference showing? Is it W1 & W2?
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@Eric Murphy sorry im not sure, I can check with my accountant on Monday, he just sent me this to inform me of the variance; “Per the ATO STP Reports please note the following FY25 totals:” …where he gave me the amounts, which are incorrect and different to the EOFY finalisation figures I submitted. After investigating I found that the variance is due to the last payroll submission of the financial year not being included. (Although it was included in my Reckon EOFY finalisation). Confirming also that this last payroll submission was done and paid on Fri 27/6/25, within the time frame to be included.
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Morning @TLee
I agree with Eric above, if we can get a bit more info on where specifically your accountant is seeing this variance it might give us a better idea on determining what's happened.
In the meantime, if you go the STP page in Reckon One do you see a successful STP submission for that last payrun of the year?
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Hi @Rav , thanks for yr response. This morning I checked on Reckon Payroll and discovered that on the list of payruns the last payrun of the financial year status shows DONE, with all figures showing correctly. Also the EOFY finalisation figures are correct and include this last payrun. But when I look at the list of STP Submissions it shows an update for that particular payrun date and both Gross and Tax amounts are showing 0. So I’m not sure why that has happened and how to rectify? If I try to resubmit it, wouldn’t the EOFY finalisation figures be affected? I’m happy for you to email me directly if you like? Thanks, Tania
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Hi @TLee ,
When you lodge an Update Event, such as to reflect changes to an employee’s Year-To-Date (YTD) balances ,it updates employee data only. These submissions do not include employer-related components, which is why the ATO Portal will show that an entry has been received, but won’t display any detailed figures like Gross or Tax.
The figures you’ve correctly submitted in the EOFY Finalisation (which includes the last pay run) are what will be reflected in the employee’s income statement on MyGov.
So in short:
- The $0 figures in the Update Event are normal if no YTD changes were made.
- Resubmitting the Update Event won’t affect the EOFY Finalisation figures.
- No action is needed unless you need to correct YTD balances.
Please let me know if you need any further clarification.
Regards,
Reeta
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Hi @TLee
When you say that final pay run (not the EOFY finalisation) is showing $0.00 does it appear like this with the Type listed as Update rather than Pay Run?
If so, then that is the cause here and the info from @Reetaabove is correct. An update event-type submission is only used to amend employee balances, it does not contain any employer data.
I'm going to assume that the variance your accountant is seeing is in the prefill for W1 & W2. I'd highly recommend reviewing the info here - #TipTuesday - What's in an STP submission? 💻
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No worries at all.
You've got a choice, you can either send the STP submission for the pay run again, as a normal STP submission this time and not an update event. If you do that, you'll also need to send the EOFY finalisation again. This will update the prefill on the ATO Portal and also re-finalise the employee balances.
Alternatively, and this is probably what I would recommend, just amend the prefill balances in the W1 & W2 fields in the ATO Portal.
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Hi @Rav, just an update and need some clarification please. I spoke with my accountant and I went with yr Option 1. I resubmitted that particular payrun and it shows SUCCESS on the STP report.
I have another similar entry for last financial year, that needs correcting. An update with an included manual entry of an extra $100 PAYG for a staff members pay (by their request)is not showing on the STP of that payrun. How can I rectify this without changing any other figures? All other figures are correct so I’m worried if I resubmit the entire payrun it will increase (double up) the other figures and not just add the $100 Tax to one of the employees.Once this is rectified, do I have to redo the EOFY finalisation even though the one I submitted last month is showing the above figures included already?
With Thanks
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Hi @TLee
An update with an included manual entry of an extra $100 PAYG for a staff members pay (by their request)is not showing on the STP of that payrun.
Where are you seeing this specifically? In the ATO Portal or in the STP page within your Reckon One book?
Also, when you say it was an update, do you mean you edited the original pay run and sent an update event submission?
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When I checked the STP confirmed list on Reckon on 27/6/25, I discovered that a payroll back in Nov hadn’t been included in the STP list. So I submitted it again. Like the other entry above it’s also now showing 0 for Gross and PAYE amounts. Would I be correct in handling it the same way, and not calling it an update, and submitting the entire payrun including the additional $100 tax amount.
Once completed will need to redo the EOFY finalisation? I’ve not looked as yet where this is done so maybe a stepped location would be helpful please.Also, a glitch in the program. When you open up the Payroll tab on the left menu items, theres a drop down, it allows you to press one of the items on the dropdown, but not subsequent. I need to go to another tab first then back to the Payroll tab to choose the next menu item. (See photo attached)
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When I checked the STP confirmed list on Reckon on 27/6/25, I discovered that a payroll back in Nov hadn’t been included in the STP list. So I submitted it again. Like the other entry above it’s also now showing 0 for Gross and PAYE amounts. Would I be correct in handling it the same way, and not calling it an update, and submitting the entire payrun including the additional $100 tax amount.
No I wouldn't do that. Each time you send a normal payrun STP submission its going to impact the W1 and W2 balances that the ATO prefill from the submissions. From what you've described so far, you've done everything correctly.
Please bear in mind, update event submissions do not contain an employer component, all they do is amend an employee's pay balances which is why it shows $0.00 for gross and tax on those submissions.
Based on where you are at now, in my view I think the only thing that may be out of balance is the W1 & W2 prefill balances in the ATO Portal and there are reasons why that occurs as mentioned previously above. If that's the case, then are two things that you (or your accountant) need to do;
- Send a new EOFY finalisation since you mentioned you sent a new STP submission
- If the prefilled W1 and W2 balances in the ATO Portal are not what you, or your accountant, expect them to be, edit those fields to correct the prefill.
If I'm mistaken in terms of my observation then please let me know.
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Reckon Staff 
