Problems transforming a model

I'm having issues when I want to import a step file into a program that has already been created.

Recently I wanted to add to a program that had already been created so I imported the step file into the program and tried to transform the model to suit the main part alignment so any point I took on the newly imported model was then relevant to the alignment.

I transformed the part so it was rotated the correct way, then I took a point on the face of the part to find the Z and a circle to find the centre. When I transformed the model the correct amount on the 'Z' that was fine, the issue was then when I tried to move the model the appropriate amount on the X & Y. I would move it to the centre according to the figures that my measured circle gave me, but after I transformed the model you could see it still wasn't correctly centred. I would take another circle and it would still show the centre of the model was slightly out to the centre alignment. I would then transform the model again to suit but it would never quite be centre!

Is there a reason why this is happening? What am I doing wrong lol?

Any help appreciated.

Cheers,
Gary