Eclipse 3.1 is not supported as this time and is slated for final release in the May timeframe of next year, we will look intos upporting it once it hits RC releases.
In the mean time we highly suggest using Eclipse 3.0.1 as its a very stable combination with MyEclipse 3.8.2. As a last resort if you really want to try MyEclipse with Eclipse 3.1, you can grab the Manual install and follow the instructions included with it to install MyEclipse manually (its extremely simple).