This looks like a blending issue: white rectangles are drawn inside a Darken transparency group that's inside a (otherwise empty) Normal group that's inside the page's main content group. Because the Normal group's (empty and transparent) background is used for blending instead of the page's content group's background, Darkening fills the Normal group's background which is then overlayed over the content. A solution might be to flatten a group's backdrop before blending.

FYI: http://code.google.com/p/sumatrapdf/source/detail?r=2843 implements non-isolated transparency groups for our GDI+ renderer.

Correct. We don't support non-isolated and knockout transparency groups in our renderer, nor do we plan to implement it anytime soon. We do provide the isolated and knockout flags to the device interface, as you've already seen and used for your gdi+ device.

This is pretty much fixed now.

There is a small remaining issue with the boxes losing the bounding lines at high resolutions, but this seems to be due to the stroke width being too small in the file.