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[the_brain]

Swany,

I'm working with PitStop for years and was intreged by your issue. So, I've create a small file and did your steps

It works fine on a small file, so it will be related to the content. Are there form objects or clipping paths in the file?
Don't forget that some object could have there origin outside the media, which will change the center position. This because the content bounding box is used to position.

Cheers.