A formation flight controller that had been previously developed for flight testing was used to investigate the controller performance in four control reference frames. The frames investigated were the tanker body frame, formation frame, wing body frame, and wing wind frame. This paper details the aerial refueling problem as a specific use of a cooperative formation flight controller. The details and drawbacks of each control reference frame are presented along with a description of the model and control laws used for the simulations. The stability of each frame was analyzed by simulating an aerial refueling flight profile. Once implemented, the gain coefficients for the control laws were tuned to each individual frame to reduce position errors, but maintain stability. Analysis of the four reference frames under identical flight profiles led to the conclusion that the tanker body frame was the frame with the most desirable performance.