The CPU power connections do not need to match perfectly with the ports on the motherboard. It would be normal to see them keyed slightly differently. This will not cause any harm to your system. The rounded off pins would still be able to fit inside the square holes, but not the other way around. The rounded off connections are there to ensure that you do not plug the connection upside-down.

Included below are pictures of the connections. Do keep in mind when viewing these pictures, that we are looking at a front view of the ports. The cable would be flipped horizontally to enter the port.