i'm pretty sure she has the aquatic variety. aka... hermianthus glomeratus.... usually known as hermianthus micranthemoides (however you spell it). I have it as a carpet in my tank.
common plant names can be misleading~ lol
I've never actually seen a case of java fern root/rhizome rot... I have some of mine growing in just plain old soil with buried rhizomes and there doesn't seem to be a problem. I'm thinking it might just be a myth :P
but do take it out of the gravel, just in case ;)