Question: Client has earnt above higher education loan repayments threshold however LodgeIT is not picking up the reportable fringe benefits amount so there is no amounts payable in the estimate tab. This client should be paying tax not receiving a refund.

Answer: Check if the person has dependants? A low family income does not require compulsory repayments.

https://www.ato.gov.au/individuals/study-and-training-support-loans/compulsory-repayments/

Question: Individual tax return taxable income is below the repayment threshold for higher education loan repayments however the estimate tab shows a payable as this is charging my client for the loan which should happen. Attachment to explain further. Client should receive refund.

Answer: Repayment income (taxable income ($37794) plus fringe benefits ($29998)) is above the threshold. LodgeiT calculation is correct.
Learn more - https://www.ato.gov.au/tax-rates-and-codes/study-and-training-support-loans-rates-and-repayment-thresholds
Note repayment income (RI) is taxable income plus any total net investment loss (which includes net rental losses), total reportable fringe benefits amounts, reportable super contributions and exempt foreign employment income.

Note: Repayment cannot be more than accumulated debt. Ie, Accumulated TSL debt is recorded as $4331.60 hence repayment has the same amount too.