TERS / IRP5 query

Hi, I just started with a new company and a query was raised w.r.t. personal tax assessment not reflecting to be correct.  I have an employee that has to pay SARS R10k back and in the past he as always received a refund.  The only difference I can notice is the TERS amt code 3724.  From what I understand is that the employees were paid direct and the TERS was not paid through payroll, however the IRP5 code was received from VIP and the amounts recorded. See below what snip shot.......... please can you assist with sorting out this dilemma?  The company has been informed to not proceed with their assessments until further notice.  Looking forward to hearing from you.