As Kirk said, load the camera correctly, wind until (1) appears in the red window on the bottom and then close the window, and engage the counter by pressing the button above the crank. Then you're ready to go.
The crank will move less and less for each shot you take, to compensate for the taking spool getting thicker, to give even spacing between the pictures.
Don't assume something is wrong with the camera before you have used the counter correctly! I've used Efke, Kodak and Agfa films with my Rolleiflex Standard cameras with no problems with overlapping.
By the way, the reason for the red window being on the bottom is that 120-film (also called B2 6x9) only had markings for 6x9 back then, so that's what you see through the red window. The number (1) for 6x6 will then be in the correct position.
The early versions of the Rolleiflex Standard had another red window on the back, for use with 117-fim (B1 6x6). 117-film gave you six 6x6 shots on a roll.