MYOB PAYBY Amount doesn't match invoice

I have recently enabled MYOB PAYBY (Online Payments) now that we've been able to opt out of the BPAY option, and we have customer pays the surcharge option enabled. 

The problem is when I got the first payment come through, the amount we received in our bank account doesn't match the invoice amount and also it didn't automatically match to the invoice that was paid.  I have finally tracked down the Online Payment transaction list where I can see the details of the payment (which by the way is very convoluted considering everything else we do is inside the AccountRight application).

So the real problem is, the MYOB Transaction into our bank was $24.56, but the invoice amount was $24.50, so it's understandable that the auto matching didn't work because they paid us 6 cents more than expected.  But the question, is how the heck do we account for this mismatch and how do we write off the 6 cents, but more to the point how does this happen?  I can see that there was a surcharge of $0.69 and a surcharge GST of 6cents, so how is that related?

All of this time spent trying to sort that is clearly not worth the effort for an invoice of $24.50!