Once a quarter, a global correction of orders is performed from the moment of starting working with the system to the end of the current reporting period. This usually compensates you if you paid more for the system services, especially if you carried out returns and refunds on orders during that time. But also sometimes there are cases when you need to pay the difference – if you have not paid in full for previous reporting periods (eg. if you got some new unaccounted refunds from eBay during that period etc.)
You can verify the accuracy of the calculations by comparing the amount of all payments made (minus bonuses) in the My Payments section and the total profits for the same period in the Sales Overview report. This is a “running” number (gets changed with each refund, return, etc.), so a small error should be expected expected – it will be cleared during the next quarterly correction.