Capital One Credit Card Assessing late fees when you pay on time Internet

I just want to start by saying that I pay my bills! I pay my Capital One credit card usually 5-10 days before the due date (online) and I ALWAYS pay over the minimum balance. Like they did to all their customers, I went from 12% to 17% because of the changing economic climate. I have since transferred most of my balance to a credit union card that offers a MUCH lower interest rate. I keep a small balance on this card to keep up appearances since this is my oldest credit history. Since I transferred a large sum of my balance I have paid 2 payments on the day they were due, and both times they have assessed me a $39.00 late fee on the day it was due. I do not understand this! If a payment is authorized on the day it was due, but the funds came out the next day, how are they able to do this? If you send a check in the day it was due, obviously you're not getting your funds until the check clears... so I don't understand why this would be different for an online payment. I have had BOTH late fees waived, but I just want to put this warning out there just in case someone doesn't look at their statement like a hawk (like I do!).