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It's hard to say for sure. It might be related to the type of bounding box. The default bounding box is called Visual, and it includes the width of the stroke. It also makes Inkscape include the width of the stroke in object dimensions. Most people who use Inkscape for cutting, like you, switch to using the Geometric bounding box. With that, the stroke is irrelevant to the dimension.
I suspect that Inkscape is not moving the objects, but instead is compensating for the stroke, or maybe changes of the stroke width. Try switching to the geometric bounding box, and see if that fixes the problem.
Edit menu > Preferences > Tools > Geometric bounding box
If that doesn't fix the problem, we will investigate further.