Are you sure the container is reloading the same JAR twice? Perhaps you have the JAR in the classpath twice under two different names...
If you're using JBoss, try re-extracting JBoss and re-deploying your EAR/WAR and doing an 'ant clean deploy'.
It seems like it's something pretty basic related to classpath/classloader issue...
I figured out why this was happening. I was placing the seam.properties file in the ear root. I moved it to the ejb root and everything worked fine.