Gear ratio ?
Yes, having the speedo calibrated for the wrong gear will throw the speedometer off and thus will make the RPMs appear to be different at a given speed.
BTW, (assuming your speedo is programmed correctly and that you have stock height tires) your RPM would be 2931 in direct (4th gear in your case) at 60 MPH with 3.73 gears or 3221 with 4.10s.

