Comment 46 for bug 1546328

Looks like the purpose of that code is to make the application singleton. There are lots of solutions for this task that do not require X11. Here is a very small library that qjackctl can probably use or embed: https://github.com/itay-grudev/SingleApplication.

As a quick and temporary fix, maybe that functionality can be disabled? It looks like --enable-xunique=no to configure may be sufficient.