JBoss Tools 4.2 (for Luna) doesn't deploy all .class

The problem I'm facing is that when I run/debug my aplication from Server view in Eclipse the jboss plugin doesn't deploy all the .class files, thus I get ClassNotFoundException.

I've tried cleaning the project, cleaning jboss, remove temporaries but nothing works. The not found classes are random.

For Eclipse 4.3 everything works fine, although this issue usually happens but I can solve it with a Project -> Clean

As a context, I've installed Eclipse Luna (also tried STS 3.6) and added Jboss Tools plugin 4.2.0 Beta 3 (I've installed only Jboss AS component). The jboss servers I tested were JBoss 7.1 and Wildfly 8.1.

I also tried building the war outside Eclipse and deployed manually to JBoss and everything works fine.