I break out part of a mesh to a new object (P) and then link duplicate it (Alt-D) and move it to a few places (G).
Then I hit render, and the objects are all bunched up where I placed the last one… but in the viewport it’s fine… until I save, close and re-open the file… then they become bunched up in the viewport as well.
Do they by any chance have a keyframed position? Blender would store their new location only temporary until you switch frames, render, exit or keyframe the new coordinates.
That feature may be useful to movie animators, but working with architecture and product visualization I must say that I loathe that behavior 99.9% of the time…