Another diference between using command line and JBoss tools is that you might be deploying compressed archives on command line and exploded archives in JBoss Tools.
You can test if that has any effect by changing the server settings (double click on the server in eclipse, get the sever editor) and enable the "Deploy compressed archives".
Concerning java vs javaw then yes the only difference should be the console but JBoss logger does not require a console - it can log to files too.
p.s. Questions concerning specifics about JBoss AS/hornetq and how it might be affected by java vs javaw is best ansked for in the jboss as/hornetq forums.