You will get "white boxes if your missing a graphics file/dds file.
I know when we know more we tend to over look the obvious or first steps (I know I do atleast)
If you haven't already done so you may want to delete your eq2map files (the actual xml and etc, not the program files) and let it pull them all down again.
My version uses the following file for icons on the map.
icon_map3.dds which is located here: customui\images\icons