I notice in the bottom pic - you have your java fern's rhizome (roots) buried in the substrate. This plant does much better when the roots are tied to a bit of driftwood or a rock, as they may rot when buried.
Java fern always tends to look a bit manky after moving tanks, and gets brown spots when ready to reproduce (I see yours already has baby plants growing off the longer leaves) so don't worry if it looks a bit like that for a while, it'll pick up under adequate light.
Anubias also does better tied to rock or wood. Both plants are epiphytic (semi-parasitic) meaning they don't grow in substrate but on the branches of other plants.
If you want plants that will feed on the substrate, try some true aquatic stem plants (wisteria, elodea, etc) or swords - swords will need root tabs after a while and can grow huge, but they're great for the water.
Last edited by Aus; 08-21-2012 at 04:23 AM.