Documents which vary in resolution (PPI) will show variations in sizes when moving things between them.
Ensure both documents are set to the same PPI.
In addition, you will want to uncheck Resize Images During Place in the Preferences (General).
As suggested, I selected all files in the INDB panel by clicking the last file then, while holding the Shift key, selected the top file. I then clicked the menu icon in the upper right corner of the panel (three horizontal bars), selected "Update Numbering," then selected "Update Page and Selection Numbers." It worked! Yay!
The only explanation I can come with is related to Snapping, Grids and Rulers.
The unexpected behavior could come from a combination of several things:
You have turned on Snap to Grid.
You have turned on Snap to Pixel.
Your grid has unwanted settings. Check Edit > Preferences > Grid and see if Gridline every and Subdivisions is set to what you want.