There was a bug in 1.0.0 (fixed in 1.0.1) where if the path contained spaces then you would get something like this error. (URL encoding had the spaces as %20 and so some classes where not found in the classpath.
Can you find and show me parts of the log...
7/01/2009 10:39:42 com.avaje.ebean.Ebean$ServerManager createServerFactory
INFO: Ebean Version[1.0.1-081216] Java Version[1.5.0_03]
7/01/2009 10:39:42 com.avaje.ebean.server.core.BootupClassPathSearch search
INFO: Classpath search hits in jars pkgs[com.avaje.ebean.meta, dbpost, com.avaje.ebean.server.bean] searchTime
The "Classpath search hits in jars pkgs..." shows where Ebean found entity beans during it's search of the classpath. I'm guessing there is some difference in the classpath setup between running in Eclipse and outside of eclipse.