Go to options and global profiler setteings and apply persistent settings.
Apply them to what? Whenever I go to Options and try to apply persistent settings, it wants me to select a profile from the dropdown. I am having the same problem as the OP in that I cannot build a profile for any of the WC dosbox games from GOG because I cannot properly link an executable. When I browse to the executable path while setting up the WC profile for the first time, what executable am I supposed to select? If I select the shortcut that installs by default, DOSBox won' open the program and just defaults to a Z> prompt.
The OP seems to have successfully understood your advice and fixed the issue, but I am apparently not as sharp as he is. I haven't used a joystick since Mechwarrior back in the 90's and I feel like an utter noob, but I am lost here.
The GOG shortcut to the WC executable seems to have additional lines of information attached, presumably to allow dosbox to automatically configure for the game as it loads, but the Logitech Profiler seems to choke up when I select that shortcut as its default executable path. This problem isn't WC specific, as I seem to be having it when trying to create ANY profile in Logitech Profiler that uses a GOG 'proprietary' shortcut to a game requiring DOSBox. So I don't seem to be able to build a profile for Strike Commander either, for example.
What am I not understanding about this? :(