Line 908 of Display.java is
glClearColor(r, g, b, 1.0f);
Having the alpha component hardcoded as 1 contradicts expected OpenGL initial state of 0.
Happily you'll never notice this unless you start rendering into FBOs and have to go spelunking through lwjgl source to find out why your output textures do not have the expected transparency.
Unhappily, fixing this by just changing the 1.0f to 0 might silently break code for people who are happy with the current behaviour. On the other hand they are relying on broken behaviour, so maybe the burden is theirs.
Fixed.