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I'm seeing a very similar (if not the same) issue when attempting to do a lookup from a Windows (XP) client to 8.1SP5 hosted on a Linux machine. It does not happen between two Windows hosts.
I noticed that it only happens when the client attempts to lookup with the thin-client jars (wlclient & friends), but not if it was using the actual weblogic jar. It seems as if the thin-client jars use a different mechanism to perform the lookup, GIOP 1.2 LocateRequest, as opposed to a NetBIOS query for the full weblogic jar; the GIOP 1.2 LocateReply seems to be corrupt (or at least it has Ethereal convinced). So, in theory you could bundle your application with the weblogic jar, which may not be a (legal) option when it comes to redistribution, depending upon your licensing agreement...
Seems like a bug to me, one that's likely never to be fixed...
I'm only about a year too late to post here. But I'm having a similar issue.
Exception: javax.naming.NamingException: Unhandled exception in lookup [Root exception is org.omg.CORBA.MARSHAL: Unable to read value from underlying bridge : Mismatched serialization UIDs : Source (Rep. IDRMI:weblogic.jms.common.DestinationImpl:3200172DE10962BC:9D20B7772483C45B) = 9D20B7772483C45B whereas Target (Rep. ID RMI:weblogic.jms.common.DestinationImpl:0000000000000001:54A6C89D6A65FBFC) = 54A6C89D6A65FBFC vmcid: SUN minor code: 211 completed: Maybe]
I'm trying to use JNDI to get context for a JMS Topic