Actually this might be a different problem to what I was thinking... in that it looks like the connections look to be in autocommit=true mode.
That is, it could be that Ebean is assuming that the connection pool by default creates connections with autocommit=false. If Ebean is not checking this that could be considered a bug...
Are you able to check that the DataSource is in fact defaulting autocommit=true... and can you set it to autocommit=false? Perhaps this is actually what you meant but I didn't understand?