How did you plant the java ferns? I think you might be planting it wrong since you mentioned you planted it in your substrate. The rhizomes need to be exposed for it to survive which is why you'll normally see it attached to rocks and wood. They'll die when their rhizomes are buried.
I currently just use my stock led and filter (cheap and low-tech) from my Chi and have had positive results with java ferns, moss, anubias, banana plant, wisteria, rotala (they just weren't red), anacharis, and ludwigia repens. No co2 and just Floramax as my substrate. I'm currently experimenting with rotala butterfly at the moment :P