I ran gdb and attached it to a running instance of the program, I got these two lines on exiting gzdoom:
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Program received signal SIGSEGV, Segmentation fault.
0x00007fcaacc41603 in SDL_JoystickClose () from /usr/lib/libSDL-1.2.so.0
This could seem unimportant if not for the fact that it prevents configurations from being saved.