I've got something like this going too - I'm calling it "the black death." Mine were gorgeous, then I started a new tank, and took only cuttings, re-tied them to the same drift wood - and now they're disintegrating. And it appears to be spreading to other plants it touches - a crypt, specifically.
Hi there. I've had the same exact problem anytime I've ever tried to grow java fern. It's like parts of the leaves on all of the leaves, (atleast on my plant) turns "black and dry." I had a friend who tried growing it too and the same result.