Hi there,
I've never kept java ferns, but I can take a stab at this for you. The leaves turning black is definitely not a good sign, unless it's just the occasional old leaf (which is then pretty acceptable ... just remove the leaf carefully so it doesn't degrade your water conditions. Some prefer to see if the leaf will sprout baby plantlets first, as many dying leaves will try to go out with a bang, so to speak, producing a bunch of little asexual plantlets).
From what you say, though, it sounds like many of your leaves are turning black, which is definitely a bad thing, especially if it's new growth and not just old. My guess is that it's definitely not a light deficiency problem. As you said, java ferns are low light plants and can thrive in light conditions between 1-4 watts per gallon, from everything I've read. Some people find their plants can grow equally well in high and low light, but others have found that high intensities of light result in "burning" on the leaves, usually in the form of translucent patches.
One thing I suppose I should mention is that if the "black" on the leaves is just a series of small spots on the underside, this is not a bad sign! Ferns reproduce sexually by making sporangia, and your java fern is just trying to reproduce. This is different than the asexual reproduction that you get the baby plantlets from. It's unlikely that your java fern will reproduce sexually underwater, though, and most likely the leaf will slowly die -- though often not before creating a host of asexual youngsters! Again, you may want to remove black or dying leaves from your tank, for the sake of aesthetics and your water conditions.
If the black on the leaves is not little spots and the whole leaf is black, it means that leaf is dying/dead. Many things can cause leaves to die, among them sudden changes in water conditions (have you had to add medication or algicide recently? Remember that it can take a long time for the effects of these to show on slow growing plants) or a lack of nutrients. It may be an iron deficiency, but plants need a number of nutrients, so potassium and even
nitrate may also be culprits. If you notice any yellowing of the leaves, make a note of where it is and what age of leaf (old leaf, young leaf, tip of leaf, edges, veins, etc) as this can help pinpoint what nutrients may be lacking. Black leaves, unfortunately, do not provide many clues.
If you suspect that it's a pathogen of some sort, you should immediately remove all dead or dying portions of the plant to prevent the disease from spreading.
Hope this helps even a little bit! The good news is that java ferns have been known to come back from a lot, so even if your plant seems a lost case, if you can find the source of the problem and fix it your fern may make a miraculous recovery!
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