The current 64-bit version just applies a dark skin. It's not too hard to fix--you just have to do it manually. If you don't mind the default theme, you can just rename the file C:\Program Files\Inkscape\etc\gtk-2.0\gtkrc to something else. That will disable all themes. It gets a bit more complicate...

Hiding a layer doesn't remove it from the file. It only makes it invisible. You have to delete a layer to get rid of it entirely. So the way you could save each layer separately would be to Save a Copy of the full file first, then delete all layers except one, vacuum defs, and then Save As. Then und...