Created attachment 214278 [details]
HTML file highlighting the problem
When a flow consisting of empty boxes (say, <div>s) with a set geometry (width & height) is flowed in a region, boxes flowed after an unforced break will be laid out as if they had margins, even though they don't.
Doing the same but with the boxes also having text contents will lay out correctly.
In the attached file, you should see two rows, each with two horizontal green rectangles with black borders.
The green rectangles are made out of boxes flowed in regions.
The boxes in the top right region are shifted downwards even though there's no styling to cause that. Replicating the markup but adding an 'x' in each box produces a correct rendering (bottom row).