Same problem for me, but:
For some reasons there is an untransparent "color" (what you discribed as blank) on the day.gif which overlays the map (but with fragments to be seen if the transperance is not set to complete solid). This happens with many skins on my PC!
I have the freeware XnView Pictureviewer (3.6mb, www.xnview.de ) installed. This viewer can show the colorinformation (hit view -> Display Color Information) of the blanc part: "#FEFEDE" which is also mentioned in the freedrive skin.ini :
#transparent 0 to 10 (0 - clear , 10 - solid)
transparent = 8
#FEFEDE seems to be not transparent ON MY PC.
If I now open a box on the blank area and Edit -> clear this box, XnView shows the color #000000. Now save as day.gif and edit the pixelmask to pixelmask=000000,000000 in the freedrive skin.ini
Clear the section for the night.gif the same way, too.
#000000 is transparent somehow! This is how it works on my PC.