Hi Hema,
Make sure you have positioned the objects on the project origin before saving as a custom junction.
If you have done so and it still is offset to one side, check in the 3d script and remove any extra 'add' commands at the start of the script (along with the corresponding 'del's at the end).
I did a quick test and for some reason no matter how I saved it, it was still offset to the side until I edited the code and removed the 'add's.
Hope that helps.