Known issues in Staffology Payroll

We do our best to keep everything running smoothly, but sometimes things happen.

This page lists the issues we know about, along with any workarounds and, where possible, an estimated time for a fix. We keep this page updated, so if something isn’t behaving as expected, this is the best place to check first.

Fixed issues lists what we've resolved within the last 6 months.

*Estimated fix dates (ETA) are subject to change.

Issue: Deleting Supprun removes HMRC His Majesty's Revenue and Customs is a non-ministerial department of the UK Government responsible for the collection of taxes, the payment of some forms of state support, the administration of other regulatory regimes including the national minimum wage and the issuance of national insurance numbers. liabilities
Information: If a supplementary pay run has been created and the subsequently deleted the HMRC liabilities are also being removed and no value will appear for the period.
Workaround: After the supplementary pay run has been deleted re-open the main pay run and re-finalise.
ETA*: 6th March
Severity: Medium

Issue: Sup Run Paycode created after main run
Information: If a paycode is created after the main run and a sup run is then carried out the paycode cannot be selected within the sup run for processing.
Workaround: You can include the new paycode by re-opening the main run and then finalising the main run before the sup run is carried out.
ETA*: 28th February 2026
Severity:Low

Issue: Linked EPS Employer Payment Summary is an RTI online submission sent monthly if, you are reclaiming statutory payments, claiming Employment Allowance (EA is only reported once per tax year), reporting Construction Industry Scheme (CIS) deductions or reporting how much Apprenticeship Levy is due. The EPS is also used to report if no employees will be paid for a whole tax month or longer. with Statutory Recoveries (Ref: 89089)
Information: For linked EPS submissions covering multiple companies, statutory recovery amounts are only included if the EPS is submitted from a company that has a recovery. If the EPS is submitted from a company without a recovery, no recoveries will be reported.
Workaround: Submit the EPS from one of the companies with a statutory recovery amount.
ETA*: 28th February 2026
Severity:Medium

Issue: Apprenticeship Levy The Apprenticeship Levy is a UK tax on employers which is used to fund apprenticeship training. It is payable by all employers with an annual pay bill of more than £3 million, at a rate of 0.5% of their total pay bill. It is collected through PAYE alongside other employment taxes. incorrect after sup run. (Ref 88684)
Information: In cases where the Apprenticeship Levy is applicable and a supplementary pay run has been completed, the Apprenticeship Levy calculation is incorrect. This occurs because the Gross NI year-to-date value is duplicated for employees appearing in the supplementary pay run.
ETA: ASAP
Severity: High

Issue: NI Savings appears to be half of what it should be. (Ref: 86817)
Information: NI Savings is appearing as half of the expected value. This is due to the worker group A group of employees who have the same pension contribution level and other settings. being incorrectly included, as the system is checking whether NI Savings is ticked or whether the NI Savings percentage is greater than 0. Because the field defaults to 100% even when not selected, it is being pulled in incorrectly.
Workaround: Select the second worker group as NI Saving, amend the % to 0, then clear the NI Saving selection.
ETA*: 31st January 2026.
Severity:Low

Issue: The HMRC payment value on the required payments report that is being received via the auto email option is displaying an incorrect figure. (86176)
Information: When comparing the HMRC value on required payments report that is being received via the auto email option is displaying an incorrect figure compared to the report that are displayed on screen or downloaded directly from Staffology showing the correct figures.
ETA*: 31st January 2026.
Severity:Low

Issue: Re-opening a payroll run with auto submit FPS Full Payment Submission is an RTI online submission to be sent on or before each payday. This informs HMRC about the payments and deductions for each employee..
Information: When Auto-Submit FPS is enabled and a payroll run is reopened, the late reason is not currently not being sent.
ETA*: 31st January 2026.
Severity: Medium

Issue: Payrolled benefits appearing incorrectly on payslip A statement provided by an employer to an employee, detailing their wages, deductions, and net pay for a specific pay period.This is a legal requirement under the employment rights act and should be received on or before the pay date. pdf. (78502)
Information: Payrolled benefits are incorrectly displayed on the payslip PDF even when the “Show Payrolled Benefits on Payslip” feature is not enabled.
ETA*: 31st January 2026.
Severity:Low

Issue: Previous Payroll Code appears incorrectly in FPS submissions. (83847)
Information: Previous Payroll Code continues to appear on every other FPS submission instead of only the first one after it is added.
ETA*: 31st January 2026.
Severity:Low

Issue: Delay in Displaying Updated Employer Information via API input.
Information: We are currently experiencing a delay in how updated employer information is reflected on the front end of the application. While the system confirms that updates have been successfully made and these changes are visible through the API, they may not appear immediately on the user interface. We are actively investigating the cause of this delay and working to ensure data updates are reflected promptly moving forward.
ETA*: 31st January 2026.
Severity:Low

---

We are actively working to resolve these issues and will release fixes as soon as possible. *ETA dates are subject to change.

History

Fixed issues lists what we've resolved within the last 6 months.

Severity	Description
High	Large impact on employees and can impact the payroll run.
Medium	May take additional time to workaround or complete the payroll.
Low	Should have a minimum impact on the day to day running of the software.