Regarding the external axis of a customised mechanism

Design

I have 2 customised mechanical units. One is basically 3 axis robot gantry and other is a 2 axis cradle type positioner. When I create virtual controller I first include only the robot and include options like multi move coordinated in it. Then using external axis wizard I select the robot and the 3 axis gantry and use the activation relay option and then I setup the 2 axis cradle type positioner using activation relay wizard. 
When I setup the 3 axis gantry the limit of my axis are correct that is they start from 0 but when I setup the 2 axis cradle type positioner my axis values of the gantry start from negative of the total stroke. Why is this so and how to avoid it?
Eg Initially when my 3 axis gantry is setup the limit is from 0 to 5000. But when I setup the 2 axis cradle type positioner the limit of the gantry become -2500 to 2500.
Thanks for time and help.