I agree with myexplodingcat. I believe what you are seeing is a severe phosphate deficiency. Didn't want to chime in too quickly as I didn't have a solution for you.
Depending on your budget, Seachem makes a product called Flourish Phosphorus that will add phosphate to your water. You may consider giving that a try.
Something else about JF's is they like to be in a current. They are almost exclusively a water column feeder. Like some bacteria, the flow across the surfaces of their leaves enables them to more efficiently draw nutrients they need from the water.
Java Ferns are a hardy species, but I have found them to be sensitive to nutrients in the water. If something is lacking, my java fern tells me first.