Settlement amount increase because I paid in 2 instalmements 2 days apart

Please could you assist me, I pulled a settlement letter on the 2nd of Feb and settlement amount was R 6251.58. I made a payment of R 2000 on the 02/02/2018 as this is my transfer limit. On the 4th I made another R 4000.00 payment. On the 5th I sent a email to ********** confirming that my outstanding balance is R 251.58. Amelia did not come back to me (still haven’t). Went on to the website to see if the money I paid was reflecting and the settlement went up with R 534.48. Now my settlement is R 796.06. As per Olivia that I spoke to this is because I didn’t settle it in one go and paid it 2 days apart its collection fees. On the settlement letter I have it states that the settlement amount is valid for 14 days. What is the difference if I pay it in one go or in 2 instalments, as long as I settle it in 14 days? please assist me in this matter