Do you have a macro program that does the tool change or is it done through the ladder? You will probably have to change your 1st reference position of the machine. If it is done via macro there is probably a position in the macro. It might use the 2nd,3rd, or 4th reference position if the tool change position is different from home position.
There is several different ways that this can be set up from the MTB. I believe in that control your first reference position parameters are #780-#783. These parameters are sometimes in metric or english. I believe it depends if you have metric ballscrews or not. These numbers are also entered with no decimal. And 4 places .0000 for english and three places .000 for metric. So if metric and you want to enter 3.1mm you have to type 3100 to get 3.1. If 31 is entered it will read as .031mm ect. You must also do a full power cycle the machine before the new value takes effect.