Hi Maciej,
Yes, I've tested the process from my web application and from the console. In each case, the process behaviour is the same.
I send you a zip with three files (a process definition and two java classes). It's a very simple process, just calling one java class.
Copy the content in the %JBPM_HOME%\examples\src folder and perform
ant -Ddatabase=oracle -Djboss.version=5.1.0.GA -Djbpm.home=%JBPM_HOME% -Djboss.home=%JBOSS_HOME% install.examples.into.jboss
then test the process "Test2".
I was not able to find exactly when the problem occurs (maybe combination with deployment and undeployment), but if you change and deploy several times the Java1 classe (just add a new System.out) at one moment the process will use the previous version of Java1 classe.
Thanks for your help