I was going to be in that position due to an improperly taxed second job and a taxable cash scholarship, but dumped a load into super to get around it. I really need that tax return and not a tax bill, so it'd be nice to get that processed properly...

Me too. They usually hit me up for about $4000 :-(

Yeah, I got the letter confirming the NOI and saw the deposit in my super balance minus 15% tax several days before I lodged my tax return. I didn't enter a value for TFN under my super contributions (just the fund name, fund ABN and amount contributed) because I couldn't find a TFN for the super fund (I assume that's for SMSFs or something), so not sure if that was an issue.

But, my ATO account has been a bit weird, random errors when logging in (not a scam) and there's a new "payments" prompt at the top of my home page even though there should be nothing outstanding

Edit: I'm a goose, the "debit" account in the payment prompt would be the amount I owe if I didn't have deductions. Sooo I have no idea why it isn't through yet. I'll wait and see...