I can't help directly, but there is likely a parameter in your controller that stores an X offset to allow for the presetter position relative to either machine home, or the spindle centerline. If that parameter is still active because it thinks the presetter is still present, it is going to keep adding (or subtracting) a fixed amount from your direct measurement. Write that parameter info down in case you get around to fixing the thing. and then try zeroing that value.
It is possible that the machine home for X may be some nonsensical value (relative to the turret position). I fooled around extensively with my Mits controller to make that machine home position correspond to the real position of my master tool T1. Since I don't have a presetter, I prefer to have the displays for machine position to be meaningful in some small way. Then I could reckon all my tool offsets relative to T1 which basically stays at zero except for tip wear.
It may be worthy of note that if you get to changing some of these parameters, you have to reboot the controller to have the changes take effect.