The issue is almost certainly the use of a single QSharedMemory key, "mem_jt9", line 10 of "main.cpp". Each paired wsjt-x & jt9 need to share a key, but the other pairs running on the same machine need different keys. Otherwise, there is a stompfest in the single shared memory area.
It might be practical to use a command line option to pass a string to modify the key. The security folks would prefer dynamically generated, difficult to guess keys. Otherwise, someone will be writing shared memory malware targeted at the application.
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