This may or may not be related to anything, but I'm curious if you specified a commit option in either of the servers.
I tested it with commit option A, and B. on JDBC level I use default XA connection to Oracle.
I guess the problem in my case in that the beans form different ejb modules with different JNDI names share the same class loader and class instance. By the way, can anybody explain me how JBoss ejb container supports pool of ejb instances? Does it separate the pool by "Application/Class Loader/class" or "Application/EJB module/Class Loader/class" (or even Application/EJB module/JNDI name/Class Loader/class). It seems WebLogic supports the second one and as I metioned before it works fine.