I'm sure this is going to be a controversial comment, but i find java ferns to be very sensitive to your water quality. All of mine used to grow okay w/ the black sections like you have until i started to use activated carbon in my canister filters. Since then, my java ferns grow much nicer looker with much less black sections. (I also don't get BBA as much, either, since i started using activated carbon.)
Maybe i'm just unlucky with my tap water and something is in it that my java ferns don't like... For me activated carbon did the trick. I'm sure there are plenty of people w/ great water from the tap that don't have this problem (of okay tap water quality) and grow great java ferns with no problem, but i'm wondering if anyone has noticed this as well... has anyone added activated carbon or switched to a purified water source like RO/DI and noticed a change in their java ferns growth?