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Update on this: Thanks to those that provided feedback, we've corrected an anomaly with the status indicator. Where a pay run had $0 super owing (nothing to pay), the status was correctly, but unhelpfully, showing as Unpaid. That's now fixed.
To be clear, that's separate from cases where super was genuinely paid, just outside MYOB (direct to an SMSF, or via a different clearing house). Unpaid in that case reflects that MYOB has no record of the payment, not that it wasn't made.
If you're still seeing Unpaid on a pay run where every employee was paid through MYOB's Pay Super, let us know via a private message - the pay run date and employee details and we'll look into it.
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