The problem is that the hibernate team keeps updating the contents of the hibernate-3.0-dtd on their site, and that pertains to the most recent HIbernate 3.1 release. Our version that we ship pertains to the version of hibernate we ship with MyEclipse (3.0.5).
In MyEclipse 4.1.0 what happened was a user reported this problem, we thought we had it wrong, pulled down the updated DTD, updated our copy then realized what was going on and reverted it.