Running the Windchill server on Java 7 is not supported until version 10.2 (at which point Java 7 is required on both client and server), so I hope you're not actually doing that.
The JIT issue I was referring to impacts old versions of Java 6 after the system has been in use for quite some time or very heavy use for a shorter time. That issue was reliably resolved (for a while) by restarting the servlet engine JVM (the method server in 10.x or the standalone Tomcat in previous versions).
