I have a similar problem. I installed Eclipse Indigo Release 2, and then JBoss Tools 3.3.1. I added a local JBoss AS 7.1.1 Final instance to Servers. I created a new Java EE Project.
Almost everytime I click on a file I get a pop-up where the details read:
"An error has occurred when activating this view
org/eclipse/jpt/common/utility/internal/StatefulCommandExecutor"