To fix this problem, go to the printer status window on your computer, then from the options menu, select Utility and then Out of Register Colors Correction.You should get a confirmation messsage and the correction will take about two minutes to complete.If you are still getting a message that calibration is occuring, make sure that the printer is not set to calibrate immediately on startup. To do this, go to the same printer status window on your computer, then go to device settings>calibration settings, and make sure the dropdown in that dialog is set to "print priority".
Are you using genuine Canon toner cartridges?
Have you tried fitting replacement cartridges?
What about replacing the other cartridges, since the magenta appears to be working ok?