The actual method class may have other dependent jar files that are not deployed properly.
 
Resolution
The method class has to be deployed to the java_methods folder. Typically, copying  the  dependent jar files to locations below ( especially # 3) and restarting the method server should fix the problem.
 
1. $DOCUMENTUM/jboss4.2.0/server/DctmServer_MethodServer/lib   
2. $DOCUMENTUM/jboss4.2.0/lib  
3. $DOCUMENTUM/jboss4.2.0/server/DctmServer_MethodServer/deploy/ServerApps.ear/DmMethods.war/WEB-INF/lib