I think the rectangle coordinates stored in the PDF file are all aligned correctly and what you are seeing is Acrobat Reader rounding coordinates to whole numbers of pixels when it is rendering the rectangles.

Sometimes it will round up, sometimes round down, and that's why you see pixel differences in the gaps.

If you zoom in you should see the gaps become more consistent. There may be some settings you can change in Acrobat's Preferences to prevent this pixel rounding.

Phil