I don't think one session of JProbe can analyse two processes at once. You may be able to run two JProbe sessions at once, one for client and one for server.
JProbe will only detect race conditions within the threads of one
Java process. If you have problems with race conditions associated with the order of processing of messages between client and server, then I think that's an issue of application design. I do not know of a tool to assist here, although that doesn't mean none exists (I'd be interested to know if one does exist).
Using JProbe on any one process, I know of no way to ensure that it only detects "real" threading problems. You just have to wade through all the potential problems that it detects, work out what is happening, and decide for yourself which, if any, represent real problems.