I recently ran across a problem with receiving a LinkageError in one of my web applications. The problem occurred when Acegi security tried to use libraries that were not yet loaded and tried to load them itself. Strangely, the error only occurred while using my RESTful API with a Spring Framework controller. If I logged in through my web interface which uses Acegi and Spring MVC, then the linkage error didn't occur.
After numerous hours of Googling around, I found a small company's JIRA issue tracker that reported the same bug, but also that it only occurred when using the security manager. After disabling the security manager on my own Tomcat instance, I found that the problem went away. I'd very much like to have a better resolution, but it's going to have to do for the time being.