Hi David,
It is not a GraphicsGrid/Row/Column. It is one Graphics object with several Inset objects because GraphicsGrid are very unreliable with styling, paddings et cetera. I can't have it rasterized though, I need the figure to be vector.
Some parts of the figure are vectorised actually; the density maps are rasterized and placed back in to the figures using Prolog. This is merely done to save some on the file-size.
Thanks for the suggestion though!
The problem though is way more general, even the simplest example goes wrong (in view and in export).
Graphics[{Pink, Disk[{0, 0}, 5]}, Frame -> True, PlotRange -> 4, PlotRangeClipping -> True]
Export["out.pdf", %]
Any more ideas? This seems like a bug, I'm open for spelunking and underground solutions creating clipping masks or hacks to fix this...