I use Intellij. I seem to remember that I had the same troubles as you at first, but they cleared up when I got the latest version of Intellij. Since then there have been no problems. But I have lots of memory and a fast machine, as well.
what version of jboss do you run? do you run it with tomcat?
I'm on a pIII 1ghz / 1 gig ram. Sometimes when i 'step over' it crashes jboss ( this started happening today ).
Win2000, ~1.7Ghz, 1Gig Rma
I am now remembering that the the problem seemed to also clear up when I went from running JBoss and Tomcat in separate JVM to running them in same JVM.