I had the same "Stop flooding" message too, but I seem to have fixed it--for now. Try this:
Right-click on an affected file. This will bring up a menu. Near the bottom of the menu is a yellow arrow and the item, "Reset". A box appears, reading "Reset selected downloads? Files will be deleted!" This is fine, just click OK; you never got the file in the first place, so you aren't losing anything. Do this for each file and reset them all. After this, I exited JDownloader and then rebooted, for the hell of it. I resumed JDownloader a couple of hours ago, and downloads have proceeded normally since then.
I may not have permanently fixed anything, though. Maybe Rapidshare has gotten wise to us, and does not want us downloading 100 MB as often as we can--even though we are obeying their rules and waiting the required waits in between. I wouldn't be surprised if they're ticked off. I hope not, I love using JDownloader, but...
I hope you guys can get your downloads going again, and my apologies if I told you a bunch of stuff you already know
EDIT: It is not a permanent fix. After two successful 100 MB downloads, I exited JDownloader, so I could burn a DVD. When I was finished I restarted JDownloader, and received "You're flooding, you're flooding" messages, all down the line.