Menu logo not transparent?

[Your Computer]

Amnesia uses targa files for graphics. There's no reason to try .png. Just open the original files and find your answer.

Actually, Amnesia uses whatever DevIL supports. If you look at many custom stories that make use of TGA files for, say, inventory items, you'll notice many that have failed to make a proper transparent image. I'd say, use whatever works from the supported list.