I had similar problem when using JBOSS 3.2.1. As a result of this problem, I always ended up getting ClassCast Exception when my servlet tries to use EJB (entity bean).
I do not know if you are having the same Class Cast Exception, I guess it depends on what you are doing.
My work around was to restart JBOSS. Then I decided to upgrade to 3.2.2. Since then, I am happy JBOSS user. Hot deployment is working like a charm.
I suggest, you try 3.2.2