I read a similar post ealier today. Are you using Eclipse 3.2.1? It's beginning to look as if it has a bug that produces this behaviour. While I was still using Eclipse on 64 bit FC6, I found a little tweak that was related to firefox - weird, but it worked. I'm afraid you'll have to google because I have forgotten what the tweak looked like.
btw, I also noticed that the problem disappeared when I switched back to gcj instead of using jdk5 or 6.