that sounds little bit strange especially when you say that it works ok on clean installation. That could mean that you don't retract process instance from working memory (session) when process is completed. In that case it will try to update variable of a process instance that is not up to date (most likely completed) but still remains in the working memory. Please keep in mind that session including all facts in it is persisted and reloaded on every server restart.
Could you please try using the RuleAwareProcessEventListener as it retracts the process instance automatically when process is completed or retract the process instance manually when you don't need it any more. Before doing this remove the session id file stored in jboss_home/standalone/tmp to enforce jbpm to create new session instead of loading one that was previously persisted.
HTH