I would like to reopen/look again at this question. I have a aerial raster file with a vector file over the top indicating specific points on the ground. I created my map, set the rotation to zero, not using WMS-layers, toggled the transparency, exported multiple times; the output PDF file continues to loose written data. The raster looks good, but the shapefile only shows up on the top half.
Has anyone else ran into this problem?
Exported Geo-referenced PDF