What are your water parameters? Hardness, pH, nitrates? And in what way are your plants not thriving? Are they all suffering the same symptoms, or a variety? What size is your tank and how well stocked is it with fish?
As
@Matt said, photos would be great.
I'm not sure about your other sword plants, but Amazons need a lot of nitrates (or nitrogen in other forms). I have a heavily planted tank, but struggle to keep Amazon swords healthy because I have tap water with very low nitrates.
Java fern, however has a low demand for nitrogen, and is slow growing. So I would expect those two plants to have different issues.
The website coynie09 linked is really helpful. Not only can it help identify why you might have algae (for example I currently have pretty much every one that has "low nutrients" as a cause), it can also help identify why your plants are failing.
Have you heard about lighting regimes that include a siesta? You mentioned that your lights are on a pattern that effects the lighting levels, but you don't mention if they have a period during the day when they are off. I am a strong proponent of having a lighting siesta. I have found that for my tank 4-5 hours with the lights off in the middle of the day works really well.